Retrieving HG38 files metadata.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Retrieving HG38 epigenomic files\n",
    "The following notebook shows how the epigenomic files metadata are retrieved."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from glob import glob\n",
    "import pandas as pd\n",
    "import compress_json\n",
    "from encodeproject import biosamples, accessions, biosample, download_urls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We specify that we are only interested in the [GRCh38](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/) assembly, are currently in status [released](https://www.encodeproject.org/help/getting-started/status-terms/#FileStatuses), have replication type [isogenic](https://www.encodeproject.org/data-standards/terms/) (there is a biological replication) and the file format is [bigWig](https://genome.ucsc.edu/goldenPath/help/bigWig.html#:~:text=The%20bigWig%20format%20is%20useful,in%20an%20indexed%20binary%20format.&text=Wiggle%20data%20must%20be%20continuous%20and%20consist%20of%20equally%20sized%20elements.)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "parameters = dict(\n",
    "    assembly=\"GRCh38\",\n",
    "    replication_type=\"isogenic\",\n",
    "    file_format=\"bigWig\",\n",
    "    status=\"released\",\n",
    "    use_multiprocessing=False\n",
    ")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We will append all the dataset while we obtain them to the following list."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "all_datasets = []"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Retrieving CHIP-seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
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      "text/plain": [
       "Retrieving biosamples:   0%|          | 0/1836 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
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     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organism</th>\n",
       "      <th>target</th>\n",
       "      <th>term_id</th>\n",
       "      <th>cell_line</th>\n",
       "      <th>institute_name</th>\n",
       "      <th>title</th>\n",
       "      <th>accession</th>\n",
       "      <th>status</th>\n",
       "      <th>assay_title</th>\n",
       "      <th>assay_term_name</th>\n",
       "      <th>...</th>\n",
       "      <th>output_category</th>\n",
       "      <th>output_type</th>\n",
       "      <th>read_length</th>\n",
       "      <th>read_length_units</th>\n",
       "      <th>run_type</th>\n",
       "      <th>schema_version</th>\n",
       "      <th>encode_version</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>technical_replicates</th>\n",
       "      <th>url</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>human</td>\n",
       "      <td>TCFL5</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF522WAN</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>human</td>\n",
       "      <td>ZNF75A</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF651OZY</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>human</td>\n",
       "      <td>ZBTB17</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF334KTM</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>human</td>\n",
       "      <td>TFE3</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF808TLR</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>human</td>\n",
       "      <td>ZNF586</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF977XAH</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2377</th>\n",
       "      <td>human</td>\n",
       "      <td>ELF1</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF036DKA</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/10...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2378</th>\n",
       "      <td>human</td>\n",
       "      <td>GTF2F1</td>\n",
       "      <td>EFO:0001203</td>\n",
       "      <td>MCF-7</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF273OEJ</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/10...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2379</th>\n",
       "      <td>human</td>\n",
       "      <td>ATF7</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF204NFC</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/10...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2380</th>\n",
       "      <td>human</td>\n",
       "      <td>CHD1</td>\n",
       "      <td>EFO:0001203</td>\n",
       "      <td>MCF-7</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF204LFY</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1, 3]</td>\n",
       "      <td>[1_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/10...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2381</th>\n",
       "      <td>human</td>\n",
       "      <td>SPI1</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF289XSX</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[2, 3]</td>\n",
       "      <td>[2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2019/02...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2382 rows × 26 columns</p>\n",
       "</div>"
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      "text/plain": [
       "     organism  target      term_id cell_line  \\\n",
       "0       human   TCFL5  EFO:0002067      K562   \n",
       "1       human  ZNF75A  EFO:0002067      K562   \n",
       "2       human  ZBTB17  EFO:0002067      K562   \n",
       "3       human    TFE3  EFO:0002067      K562   \n",
       "4       human  ZNF586  EFO:0002067      K562   \n",
       "...       ...     ...          ...       ...   \n",
       "2377    human    ELF1  EFO:0002067      K562   \n",
       "2378    human  GTF2F1  EFO:0001203     MCF-7   \n",
       "2379    human    ATF7  EFO:0002067      K562   \n",
       "2380    human    CHD1  EFO:0001203     MCF-7   \n",
       "2381    human    SPI1  EFO:0002784   GM12878   \n",
       "\n",
       "                               institute_name                     title  \\\n",
       "0                         Stanford University  Michael Snyder, Stanford   \n",
       "1                         Stanford University  Michael Snyder, Stanford   \n",
       "2                         Stanford University  Michael Snyder, Stanford   \n",
       "3                         Stanford University  Michael Snyder, Stanford   \n",
       "4                         Stanford University  Michael Snyder, Stanford   \n",
       "...                                       ...                       ...   \n",
       "2377                      Stanford University  Michael Snyder, Stanford   \n",
       "2378                      Stanford University  Michael Snyder, Stanford   \n",
       "2379                      Stanford University  Michael Snyder, Stanford   \n",
       "2380                      Stanford University  Michael Snyder, Stanford   \n",
       "2381  HudsonAlpha Institute for Biotechnology       Richard Myers, HAIB   \n",
       "\n",
       "        accession    status  assay_title assay_term_name  ... output_category  \\\n",
       "0     ENCFF522WAN  released  TF ChIP-seq        ChIP-seq  ...          signal   \n",
       "1     ENCFF651OZY  released  TF ChIP-seq        ChIP-seq  ...          signal   \n",
       "2     ENCFF334KTM  released  TF ChIP-seq        ChIP-seq  ...          signal   \n",
       "3     ENCFF808TLR  released  TF ChIP-seq        ChIP-seq  ...          signal   \n",
       "4     ENCFF977XAH  released  TF ChIP-seq        ChIP-seq  ...          signal   \n",
       "...           ...       ...          ...             ...  ...             ...   \n",
       "2377  ENCFF036DKA  released  TF ChIP-seq        ChIP-seq  ...          signal   \n",
       "2378  ENCFF273OEJ  released  TF ChIP-seq        ChIP-seq  ...          signal   \n",
       "2379  ENCFF204NFC  released  TF ChIP-seq        ChIP-seq  ...          signal   \n",
       "2380  ENCFF204LFY  released  TF ChIP-seq        ChIP-seq  ...          signal   \n",
       "2381  ENCFF289XSX  released  TF ChIP-seq        ChIP-seq  ...          signal   \n",
       "\n",
       "                   output_type read_length read_length_units  run_type  \\\n",
       "0     fold change over control         NaN              None      None   \n",
       "1     fold change over control         NaN              None      None   \n",
       "2     fold change over control         NaN              None      None   \n",
       "3     fold change over control         NaN              None      None   \n",
       "4     fold change over control         NaN              None      None   \n",
       "...                        ...         ...               ...       ...   \n",
       "2377  fold change over control         NaN              None      None   \n",
       "2378  fold change over control         NaN              None      None   \n",
       "2379  fold change over control         NaN              None      None   \n",
       "2380  fold change over control         NaN              None      None   \n",
       "2381  fold change over control         NaN              None      None   \n",
       "\n",
       "     schema_version encode_version biological_replicates  \\\n",
       "0                26            4.0                [1, 2]   \n",
       "1                26            4.0                [1, 2]   \n",
       "2                26            4.0                [1, 2]   \n",
       "3                26            4.0                [1, 2]   \n",
       "4                26            4.0                [1, 2]   \n",
       "...             ...            ...                   ...   \n",
       "2377             26            3.0                [1, 2]   \n",
       "2378             26            3.0                [1, 2]   \n",
       "2379             26            3.0                [1, 2]   \n",
       "2380             26            3.0                [1, 3]   \n",
       "2381             26            3.0                [2, 3]   \n",
       "\n",
       "      technical_replicates                                                url  \n",
       "0               [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/11...  \n",
       "1               [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "2               [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "3               [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "4               [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "...                    ...                                                ...  \n",
       "2377            [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2016/10...  \n",
       "2378            [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2016/10...  \n",
       "2379            [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2016/10...  \n",
       "2380            [1_1, 3_1]  https://encode-public.s3.amazonaws.com/2016/10...  \n",
       "2381            [2_1, 3_1]  https://encode-public.s3.amazonaws.com/2019/02...  \n",
       "\n",
       "[2382 rows x 26 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "samples = biosamples(\n",
    "    accessions=accessions(compress_json.load(\"hg38_encode_queries/chipseq.json\")),\n",
    "    min_biological_replicates=2,\n",
    "    output_type=\"fold change over control\",\n",
    "    **parameters\n",
    ")\n",
    "all_datasets.append(samples)\n",
    "samples"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Retrieving DNASE-seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
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       "Retrieving biosamples:   0%|          | 0/5 [00:00<?, ?it/s]"
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organism</th>\n",
       "      <th>target</th>\n",
       "      <th>term_id</th>\n",
       "      <th>cell_line</th>\n",
       "      <th>institute_name</th>\n",
       "      <th>title</th>\n",
       "      <th>accession</th>\n",
       "      <th>status</th>\n",
       "      <th>assay_title</th>\n",
       "      <th>assay_term_name</th>\n",
       "      <th>...</th>\n",
       "      <th>output_category</th>\n",
       "      <th>output_type</th>\n",
       "      <th>read_length</th>\n",
       "      <th>read_length_units</th>\n",
       "      <th>run_type</th>\n",
       "      <th>schema_version</th>\n",
       "      <th>encode_version</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>technical_replicates</th>\n",
       "      <th>url</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF113VII</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF577SOF</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF842XRQ</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF546MZK</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF413AHU</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1, 1_2]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2018/05...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF936BDN</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2018/05...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF414OGC</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1, 1_2]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF338LXW</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001203</td>\n",
       "      <td>MCF-7</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF924FJR</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001203</td>\n",
       "      <td>MCF-7</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF949ANK</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001203</td>\n",
       "      <td>MCF-7</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF631QXL</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001203</td>\n",
       "      <td>MCF-7</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF134COA</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/09...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001086</td>\n",
       "      <td>A549</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF280JCA</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001086</td>\n",
       "      <td>A549</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF688CJL</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_7]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001086</td>\n",
       "      <td>A549</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF985FHV</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_7]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001086</td>\n",
       "      <td>A549</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF541BTE</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF915DFR</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF743ULW</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF960FMM</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>University of Washington</td>\n",
       "      <td>John Stamatoyannopoulos, UW</td>\n",
       "      <td>ENCFF428XFI</td>\n",
       "      <td>released</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>DNase-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>read-depth normalized signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/11...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20 rows × 26 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   organism   target      term_id cell_line            institute_name  \\\n",
       "0     human  Unknown  EFO:0001187     HepG2  University of Washington   \n",
       "1     human  Unknown  EFO:0001187     HepG2  University of Washington   \n",
       "2     human  Unknown  EFO:0001187     HepG2  University of Washington   \n",
       "3     human  Unknown  EFO:0001187     HepG2  University of Washington   \n",
       "4     human  Unknown  EFO:0002067      K562  University of Washington   \n",
       "5     human  Unknown  EFO:0002067      K562  University of Washington   \n",
       "6     human  Unknown  EFO:0002067      K562  University of Washington   \n",
       "7     human  Unknown  EFO:0002067      K562  University of Washington   \n",
       "8     human  Unknown  EFO:0001203     MCF-7  University of Washington   \n",
       "9     human  Unknown  EFO:0001203     MCF-7  University of Washington   \n",
       "10    human  Unknown  EFO:0001203     MCF-7  University of Washington   \n",
       "11    human  Unknown  EFO:0001203     MCF-7  University of Washington   \n",
       "12    human  Unknown  EFO:0001086      A549  University of Washington   \n",
       "13    human  Unknown  EFO:0001086      A549  University of Washington   \n",
       "14    human  Unknown  EFO:0001086      A549  University of Washington   \n",
       "15    human  Unknown  EFO:0001086      A549  University of Washington   \n",
       "16    human  Unknown  EFO:0002784   GM12878  University of Washington   \n",
       "17    human  Unknown  EFO:0002784   GM12878  University of Washington   \n",
       "18    human  Unknown  EFO:0002784   GM12878  University of Washington   \n",
       "19    human  Unknown  EFO:0002784   GM12878  University of Washington   \n",
       "\n",
       "                          title    accession    status assay_title  \\\n",
       "0   John Stamatoyannopoulos, UW  ENCFF113VII  released   DNase-seq   \n",
       "1   John Stamatoyannopoulos, UW  ENCFF577SOF  released   DNase-seq   \n",
       "2   John Stamatoyannopoulos, UW  ENCFF842XRQ  released   DNase-seq   \n",
       "3   John Stamatoyannopoulos, UW  ENCFF546MZK  released   DNase-seq   \n",
       "4   John Stamatoyannopoulos, UW  ENCFF413AHU  released   DNase-seq   \n",
       "5   John Stamatoyannopoulos, UW  ENCFF936BDN  released   DNase-seq   \n",
       "6   John Stamatoyannopoulos, UW  ENCFF414OGC  released   DNase-seq   \n",
       "7   John Stamatoyannopoulos, UW  ENCFF338LXW  released   DNase-seq   \n",
       "8   John Stamatoyannopoulos, UW  ENCFF924FJR  released   DNase-seq   \n",
       "9   John Stamatoyannopoulos, UW  ENCFF949ANK  released   DNase-seq   \n",
       "10  John Stamatoyannopoulos, UW  ENCFF631QXL  released   DNase-seq   \n",
       "11  John Stamatoyannopoulos, UW  ENCFF134COA  released   DNase-seq   \n",
       "12  John Stamatoyannopoulos, UW  ENCFF280JCA  released   DNase-seq   \n",
       "13  John Stamatoyannopoulos, UW  ENCFF688CJL  released   DNase-seq   \n",
       "14  John Stamatoyannopoulos, UW  ENCFF985FHV  released   DNase-seq   \n",
       "15  John Stamatoyannopoulos, UW  ENCFF541BTE  released   DNase-seq   \n",
       "16  John Stamatoyannopoulos, UW  ENCFF915DFR  released   DNase-seq   \n",
       "17  John Stamatoyannopoulos, UW  ENCFF743ULW  released   DNase-seq   \n",
       "18  John Stamatoyannopoulos, UW  ENCFF960FMM  released   DNase-seq   \n",
       "19  John Stamatoyannopoulos, UW  ENCFF428XFI  released   DNase-seq   \n",
       "\n",
       "   assay_term_name  ... output_category                   output_type  \\\n",
       "0        DNase-seq  ...          signal  read-depth normalized signal   \n",
       "1        DNase-seq  ...          signal  read-depth normalized signal   \n",
       "2        DNase-seq  ...          signal  read-depth normalized signal   \n",
       "3        DNase-seq  ...          signal  read-depth normalized signal   \n",
       "4        DNase-seq  ...          signal  read-depth normalized signal   \n",
       "5        DNase-seq  ...          signal  read-depth normalized signal   \n",
       "6        DNase-seq  ...          signal  read-depth normalized signal   \n",
       "7        DNase-seq  ...          signal  read-depth normalized signal   \n",
       "8        DNase-seq  ...          signal  read-depth normalized signal   \n",
       "9        DNase-seq  ...          signal  read-depth normalized signal   \n",
       "10       DNase-seq  ...          signal  read-depth normalized signal   \n",
       "11       DNase-seq  ...          signal  read-depth normalized signal   \n",
       "12       DNase-seq  ...          signal  read-depth normalized signal   \n",
       "13       DNase-seq  ...          signal  read-depth normalized signal   \n",
       "14       DNase-seq  ...          signal  read-depth normalized signal   \n",
       "15       DNase-seq  ...          signal  read-depth normalized signal   \n",
       "16       DNase-seq  ...          signal  read-depth normalized signal   \n",
       "17       DNase-seq  ...          signal  read-depth normalized signal   \n",
       "18       DNase-seq  ...          signal  read-depth normalized signal   \n",
       "19       DNase-seq  ...          signal  read-depth normalized signal   \n",
       "\n",
       "   read_length read_length_units  run_type schema_version encode_version  \\\n",
       "0          NaN              None      None             26            4.0   \n",
       "1          NaN              None      None             26            3.0   \n",
       "2          NaN              None      None             26            3.0   \n",
       "3          NaN              None      None             26            4.0   \n",
       "4          NaN              None      None             26            3.0   \n",
       "5          NaN              None      None             26            3.0   \n",
       "6          NaN              None      None             26            4.0   \n",
       "7          NaN              None      None             26            4.0   \n",
       "8          NaN              None      None             26            3.0   \n",
       "9          NaN              None      None             26            3.0   \n",
       "10         NaN              None      None             26            4.0   \n",
       "11         NaN              None      None             26            4.0   \n",
       "12         NaN              None      None             26            3.0   \n",
       "13         NaN              None      None             26            3.0   \n",
       "14         NaN              None      None             26            4.0   \n",
       "15         NaN              None      None             26            4.0   \n",
       "16         NaN              None      None             26            3.0   \n",
       "17         NaN              None      None             26            3.0   \n",
       "18         NaN              None      None             26            4.0   \n",
       "19         NaN              None      None             26            4.0   \n",
       "\n",
       "   biological_replicates  technical_replicates  \\\n",
       "0                    [2]                 [2_1]   \n",
       "1                    [1]                 [1_1]   \n",
       "2                    [2]                 [2_1]   \n",
       "3                    [1]                 [1_1]   \n",
       "4                    [1]            [1_1, 1_2]   \n",
       "5                    [2]                 [2_1]   \n",
       "6                    [1]            [1_1, 1_2]   \n",
       "7                    [2]                 [2_1]   \n",
       "8                    [1]                 [1_1]   \n",
       "9                    [2]                 [2_1]   \n",
       "10                   [1]                 [1_1]   \n",
       "11                   [2]                 [2_1]   \n",
       "12                   [2]                 [2_1]   \n",
       "13                   [1]                 [1_7]   \n",
       "14                   [1]                 [1_7]   \n",
       "15                   [2]                 [2_1]   \n",
       "16                   [1]                 [1_1]   \n",
       "17                   [2]                 [2_1]   \n",
       "18                   [2]                 [2_1]   \n",
       "19                   [1]                 [1_1]   \n",
       "\n",
       "                                                  url  \n",
       "0   https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "1   https://encode-public.s3.amazonaws.com/2017/08...  \n",
       "2   https://encode-public.s3.amazonaws.com/2017/08...  \n",
       "3   https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "4   https://encode-public.s3.amazonaws.com/2018/05...  \n",
       "5   https://encode-public.s3.amazonaws.com/2018/05...  \n",
       "6   https://encode-public.s3.amazonaws.com/2020/11...  \n",
       "7   https://encode-public.s3.amazonaws.com/2020/11...  \n",
       "8   https://encode-public.s3.amazonaws.com/2017/08...  \n",
       "9   https://encode-public.s3.amazonaws.com/2017/08...  \n",
       "10  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "11  https://encode-public.s3.amazonaws.com/2020/09...  \n",
       "12  https://encode-public.s3.amazonaws.com/2017/11...  \n",
       "13  https://encode-public.s3.amazonaws.com/2017/11...  \n",
       "14  https://encode-public.s3.amazonaws.com/2020/11...  \n",
       "15  https://encode-public.s3.amazonaws.com/2020/11...  \n",
       "16  https://encode-public.s3.amazonaws.com/2017/08...  \n",
       "17  https://encode-public.s3.amazonaws.com/2017/08...  \n",
       "18  https://encode-public.s3.amazonaws.com/2020/11...  \n",
       "19  https://encode-public.s3.amazonaws.com/2020/11...  \n",
       "\n",
       "[20 rows x 26 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "samples = biosamples(\n",
    "    accessions=accessions(compress_json.load(\"hg38_encode_queries/dnaseseq.json\")),\n",
    "    organism=None,\n",
    "    **parameters\n",
    ")\n",
    "samples[\"organism\"] = \"human\"\n",
    "\n",
    "all_datasets.append(samples)\n",
    "samples"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Retrieving WGBS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Retrieving biosamples:   0%|          | 0/5 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organism</th>\n",
       "      <th>target</th>\n",
       "      <th>term_id</th>\n",
       "      <th>cell_line</th>\n",
       "      <th>institute_name</th>\n",
       "      <th>title</th>\n",
       "      <th>accession</th>\n",
       "      <th>status</th>\n",
       "      <th>assay_title</th>\n",
       "      <th>assay_term_name</th>\n",
       "      <th>...</th>\n",
       "      <th>output_category</th>\n",
       "      <th>output_type</th>\n",
       "      <th>read_length</th>\n",
       "      <th>read_length_units</th>\n",
       "      <th>run_type</th>\n",
       "      <th>schema_version</th>\n",
       "      <th>encode_version</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>technical_replicates</th>\n",
       "      <th>url</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF400QTE</td>\n",
       "      <td>released</td>\n",
       "      <td>WGBS</td>\n",
       "      <td>whole-genome shotgun bisulfite sequencing</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF583VWF</td>\n",
       "      <td>released</td>\n",
       "      <td>WGBS</td>\n",
       "      <td>whole-genome shotgun bisulfite sequencing</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001086</td>\n",
       "      <td>A549</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF527HXB</td>\n",
       "      <td>released</td>\n",
       "      <td>WGBS</td>\n",
       "      <td>whole-genome shotgun bisulfite sequencing</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/12...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001086</td>\n",
       "      <td>A549</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF401QUB</td>\n",
       "      <td>released</td>\n",
       "      <td>WGBS</td>\n",
       "      <td>whole-genome shotgun bisulfite sequencing</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/12...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF796NFQ</td>\n",
       "      <td>released</td>\n",
       "      <td>WGBS</td>\n",
       "      <td>whole-genome shotgun bisulfite sequencing</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/03...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF812CHG</td>\n",
       "      <td>released</td>\n",
       "      <td>WGBS</td>\n",
       "      <td>whole-genome shotgun bisulfite sequencing</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/03...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF073DUG</td>\n",
       "      <td>released</td>\n",
       "      <td>WGBS</td>\n",
       "      <td>whole-genome shotgun bisulfite sequencing</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/03...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF716NKX</td>\n",
       "      <td>released</td>\n",
       "      <td>WGBS</td>\n",
       "      <td>whole-genome shotgun bisulfite sequencing</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/03...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF872YSC</td>\n",
       "      <td>released</td>\n",
       "      <td>WGBS</td>\n",
       "      <td>whole-genome shotgun bisulfite sequencing</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3</td>\n",
       "      <td>[1]</td>\n",
       "      <td>[1_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/03...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF669KCI</td>\n",
       "      <td>released</td>\n",
       "      <td>WGBS</td>\n",
       "      <td>whole-genome shotgun bisulfite sequencing</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>signal</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3</td>\n",
       "      <td>[2]</td>\n",
       "      <td>[2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/03...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10 rows × 26 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  organism   target      term_id cell_line  \\\n",
       "0    human  Unknown  EFO:0001187     HepG2   \n",
       "1    human  Unknown  EFO:0001187     HepG2   \n",
       "2    human  Unknown  EFO:0001086      A549   \n",
       "3    human  Unknown  EFO:0001086      A549   \n",
       "4    human  Unknown  EFO:0002784   GM12878   \n",
       "5    human  Unknown  EFO:0002784   GM12878   \n",
       "6    human  Unknown  EFO:0001187     HepG2   \n",
       "7    human  Unknown  EFO:0001187     HepG2   \n",
       "8    human  Unknown  EFO:0002067      K562   \n",
       "9    human  Unknown  EFO:0002067      K562   \n",
       "\n",
       "                            institute_name                title    accession  \\\n",
       "0  HudsonAlpha Institute for Biotechnology  Richard Myers, HAIB  ENCFF400QTE   \n",
       "1  HudsonAlpha Institute for Biotechnology  Richard Myers, HAIB  ENCFF583VWF   \n",
       "2  HudsonAlpha Institute for Biotechnology  Richard Myers, HAIB  ENCFF527HXB   \n",
       "3  HudsonAlpha Institute for Biotechnology  Richard Myers, HAIB  ENCFF401QUB   \n",
       "4  HudsonAlpha Institute for Biotechnology  Richard Myers, HAIB  ENCFF796NFQ   \n",
       "5  HudsonAlpha Institute for Biotechnology  Richard Myers, HAIB  ENCFF812CHG   \n",
       "6  HudsonAlpha Institute for Biotechnology  Richard Myers, HAIB  ENCFF073DUG   \n",
       "7  HudsonAlpha Institute for Biotechnology  Richard Myers, HAIB  ENCFF716NKX   \n",
       "8  HudsonAlpha Institute for Biotechnology  Richard Myers, HAIB  ENCFF872YSC   \n",
       "9  HudsonAlpha Institute for Biotechnology  Richard Myers, HAIB  ENCFF669KCI   \n",
       "\n",
       "     status assay_title                            assay_term_name  ...  \\\n",
       "0  released        WGBS  whole-genome shotgun bisulfite sequencing  ...   \n",
       "1  released        WGBS  whole-genome shotgun bisulfite sequencing  ...   \n",
       "2  released        WGBS  whole-genome shotgun bisulfite sequencing  ...   \n",
       "3  released        WGBS  whole-genome shotgun bisulfite sequencing  ...   \n",
       "4  released        WGBS  whole-genome shotgun bisulfite sequencing  ...   \n",
       "5  released        WGBS  whole-genome shotgun bisulfite sequencing  ...   \n",
       "6  released        WGBS  whole-genome shotgun bisulfite sequencing  ...   \n",
       "7  released        WGBS  whole-genome shotgun bisulfite sequencing  ...   \n",
       "8  released        WGBS  whole-genome shotgun bisulfite sequencing  ...   \n",
       "9  released        WGBS  whole-genome shotgun bisulfite sequencing  ...   \n",
       "\n",
       "  output_category output_type read_length read_length_units  run_type  \\\n",
       "0          signal      signal         NaN              None      None   \n",
       "1          signal      signal         NaN              None      None   \n",
       "2          signal      signal         NaN              None      None   \n",
       "3          signal      signal         NaN              None      None   \n",
       "4          signal      signal         NaN              None      None   \n",
       "5          signal      signal         NaN              None      None   \n",
       "6          signal      signal         NaN              None      None   \n",
       "7          signal      signal         NaN              None      None   \n",
       "8          signal      signal         NaN              None      None   \n",
       "9          signal      signal         NaN              None      None   \n",
       "\n",
       "  schema_version encode_version biological_replicates  technical_replicates  \\\n",
       "0             26              3                   [1]                 [1_1]   \n",
       "1             26              3                   [2]                 [2_1]   \n",
       "2             26              3                   [1]                 [1_1]   \n",
       "3             26              3                   [2]                 [2_1]   \n",
       "4             26              3                   [1]                 [1_1]   \n",
       "5             26              3                   [2]                 [2_1]   \n",
       "6             26              3                   [1]                 [1_1]   \n",
       "7             26              3                   [2]                 [2_1]   \n",
       "8             26              3                   [1]                 [1_1]   \n",
       "9             26              3                   [2]                 [2_1]   \n",
       "\n",
       "                                                 url  \n",
       "0  https://encode-public.s3.amazonaws.com/2017/11...  \n",
       "1  https://encode-public.s3.amazonaws.com/2017/11...  \n",
       "2  https://encode-public.s3.amazonaws.com/2017/12...  \n",
       "3  https://encode-public.s3.amazonaws.com/2017/12...  \n",
       "4  https://encode-public.s3.amazonaws.com/2016/03...  \n",
       "5  https://encode-public.s3.amazonaws.com/2016/03...  \n",
       "6  https://encode-public.s3.amazonaws.com/2016/03...  \n",
       "7  https://encode-public.s3.amazonaws.com/2016/03...  \n",
       "8  https://encode-public.s3.amazonaws.com/2016/03...  \n",
       "9  https://encode-public.s3.amazonaws.com/2016/03...  \n",
       "\n",
       "[10 rows x 26 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "samples = biosamples(\n",
    "    accessions=accessions(compress_json.load(\"hg38_encode_queries/wgbs.json\")),\n",
    "    organism=None,\n",
    "    **parameters,\n",
    ")\n",
    "# I have manually checked that the version of the files is 3, but it is not available in the metadata.\n",
    "samples[\"encode_version\"] = 3\n",
    "samples[\"organism\"] = \"human\"\n",
    "all_datasets.append(samples)\n",
    "samples"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Retrieving ATAC"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Retrieving biosamples:   0%|          | 0/7 [00:00<?, ?it/s]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organism</th>\n",
       "      <th>target</th>\n",
       "      <th>term_id</th>\n",
       "      <th>cell_line</th>\n",
       "      <th>institute_name</th>\n",
       "      <th>title</th>\n",
       "      <th>accession</th>\n",
       "      <th>status</th>\n",
       "      <th>assay_title</th>\n",
       "      <th>assay_term_name</th>\n",
       "      <th>...</th>\n",
       "      <th>output_category</th>\n",
       "      <th>output_type</th>\n",
       "      <th>read_length</th>\n",
       "      <th>read_length_units</th>\n",
       "      <th>run_type</th>\n",
       "      <th>schema_version</th>\n",
       "      <th>encode_version</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>technical_replicates</th>\n",
       "      <th>url</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF091DNE</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001203</td>\n",
       "      <td>MCF-7</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF927YYP</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF831OKQ</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF872HBM</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF948GBJ</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF450XLU</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001086</td>\n",
       "      <td>A549</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF225UNA</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7 rows × 26 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  organism   target      term_id cell_line       institute_name  \\\n",
       "0    human  Unknown  EFO:0002784   GM12878  Stanford University   \n",
       "1    human  Unknown  EFO:0001203     MCF-7  Stanford University   \n",
       "2    human  Unknown  EFO:0002067      K562  Stanford University   \n",
       "3    human  Unknown  EFO:0001187     HepG2  Stanford University   \n",
       "4    human  Unknown  EFO:0002784   GM12878  Stanford University   \n",
       "5    human  Unknown  EFO:0002067      K562  Stanford University   \n",
       "6    human  Unknown  EFO:0001086      A549  Stanford University   \n",
       "\n",
       "                      title    accession    status assay_title  \\\n",
       "0  Michael Snyder, Stanford  ENCFF091DNE  released    ATAC-seq   \n",
       "1  Michael Snyder, Stanford  ENCFF927YYP  released    ATAC-seq   \n",
       "2  Michael Snyder, Stanford  ENCFF831OKQ  released    ATAC-seq   \n",
       "3  Michael Snyder, Stanford  ENCFF872HBM  released    ATAC-seq   \n",
       "4  Michael Snyder, Stanford  ENCFF948GBJ  released    ATAC-seq   \n",
       "5  Michael Snyder, Stanford  ENCFF450XLU  released    ATAC-seq   \n",
       "6  Michael Snyder, Stanford  ENCFF225UNA  released    ATAC-seq   \n",
       "\n",
       "  assay_term_name  ... output_category               output_type read_length  \\\n",
       "0        ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "1        ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "2        ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "3        ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "4        ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "5        ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "6        ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "\n",
       "  read_length_units  run_type schema_version encode_version  \\\n",
       "0              None      None             26            4.0   \n",
       "1              None      None             26            4.0   \n",
       "2              None      None             26            4.0   \n",
       "3              None      None             26            4.0   \n",
       "4              None      None             26            4.0   \n",
       "5              None      None             26            4.0   \n",
       "6              None      None             26            4.0   \n",
       "\n",
       "  biological_replicates  technical_replicates  \\\n",
       "0                [1, 2]            [1_1, 2_1]   \n",
       "1                [1, 2]            [1_1, 2_1]   \n",
       "2                [1, 2]            [1_1, 2_1]   \n",
       "3             [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "4             [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "5             [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "6             [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "\n",
       "                                                 url  \n",
       "0  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "1  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "2  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "3  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "4  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "5  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "6  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "\n",
       "[7 rows x 26 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "samples = biosamples(\n",
    "    accessions=accessions(compress_json.load(\"hg38_encode_queries/atacseq.json\")),\n",
    "    organism=None,\n",
    "    min_biological_replicates=2,\n",
    "    output_type=\"fold change over control\",\n",
    "    **parameters\n",
    ")\n",
    "samples[\"organism\"] = \"human\"\n",
    "\n",
    "all_datasets.append(samples)\n",
    "samples"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Combining all datasets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organism</th>\n",
       "      <th>target</th>\n",
       "      <th>term_id</th>\n",
       "      <th>cell_line</th>\n",
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       "      <th>accession</th>\n",
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       "      <th>assay_term_name</th>\n",
       "      <th>...</th>\n",
       "      <th>output_category</th>\n",
       "      <th>output_type</th>\n",
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       "      <th>read_length_units</th>\n",
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       "      <th>schema_version</th>\n",
       "      <th>encode_version</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>technical_replicates</th>\n",
       "      <th>url</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>human</td>\n",
       "      <td>TCFL5</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF522WAN</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>human</td>\n",
       "      <td>ZNF75A</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF651OZY</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>human</td>\n",
       "      <td>ZBTB17</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF334KTM</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>human</td>\n",
       "      <td>TFE3</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF808TLR</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>human</td>\n",
       "      <td>ZNF586</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF977XAH</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF831OKQ</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF872HBM</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF948GBJ</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF450XLU</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001086</td>\n",
       "      <td>A549</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF225UNA</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2419 rows × 26 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   organism   target      term_id cell_line       institute_name  \\\n",
       "0     human    TCFL5  EFO:0002067      K562  Stanford University   \n",
       "1     human   ZNF75A  EFO:0002067      K562  Stanford University   \n",
       "2     human   ZBTB17  EFO:0002067      K562  Stanford University   \n",
       "3     human     TFE3  EFO:0002067      K562  Stanford University   \n",
       "4     human   ZNF586  EFO:0002067      K562  Stanford University   \n",
       "..      ...      ...          ...       ...                  ...   \n",
       "2     human  Unknown  EFO:0002067      K562  Stanford University   \n",
       "3     human  Unknown  EFO:0001187     HepG2  Stanford University   \n",
       "4     human  Unknown  EFO:0002784   GM12878  Stanford University   \n",
       "5     human  Unknown  EFO:0002067      K562  Stanford University   \n",
       "6     human  Unknown  EFO:0001086      A549  Stanford University   \n",
       "\n",
       "                       title    accession    status  assay_title  \\\n",
       "0   Michael Snyder, Stanford  ENCFF522WAN  released  TF ChIP-seq   \n",
       "1   Michael Snyder, Stanford  ENCFF651OZY  released  TF ChIP-seq   \n",
       "2   Michael Snyder, Stanford  ENCFF334KTM  released  TF ChIP-seq   \n",
       "3   Michael Snyder, Stanford  ENCFF808TLR  released  TF ChIP-seq   \n",
       "4   Michael Snyder, Stanford  ENCFF977XAH  released  TF ChIP-seq   \n",
       "..                       ...          ...       ...          ...   \n",
       "2   Michael Snyder, Stanford  ENCFF831OKQ  released     ATAC-seq   \n",
       "3   Michael Snyder, Stanford  ENCFF872HBM  released     ATAC-seq   \n",
       "4   Michael Snyder, Stanford  ENCFF948GBJ  released     ATAC-seq   \n",
       "5   Michael Snyder, Stanford  ENCFF450XLU  released     ATAC-seq   \n",
       "6   Michael Snyder, Stanford  ENCFF225UNA  released     ATAC-seq   \n",
       "\n",
       "   assay_term_name  ... output_category               output_type read_length  \\\n",
       "0         ChIP-seq  ...          signal  fold change over control         NaN   \n",
       "1         ChIP-seq  ...          signal  fold change over control         NaN   \n",
       "2         ChIP-seq  ...          signal  fold change over control         NaN   \n",
       "3         ChIP-seq  ...          signal  fold change over control         NaN   \n",
       "4         ChIP-seq  ...          signal  fold change over control         NaN   \n",
       "..             ...  ...             ...                       ...         ...   \n",
       "2         ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "3         ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "4         ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "5         ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "6         ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "\n",
       "   read_length_units  run_type schema_version encode_version  \\\n",
       "0               None      None             26            4.0   \n",
       "1               None      None             26            4.0   \n",
       "2               None      None             26            4.0   \n",
       "3               None      None             26            4.0   \n",
       "4               None      None             26            4.0   \n",
       "..               ...       ...            ...            ...   \n",
       "2               None      None             26            4.0   \n",
       "3               None      None             26            4.0   \n",
       "4               None      None             26            4.0   \n",
       "5               None      None             26            4.0   \n",
       "6               None      None             26            4.0   \n",
       "\n",
       "   biological_replicates  technical_replicates  \\\n",
       "0                 [1, 2]            [1_1, 2_1]   \n",
       "1                 [1, 2]            [1_1, 2_1]   \n",
       "2                 [1, 2]            [1_1, 2_1]   \n",
       "3                 [1, 2]            [1_1, 2_1]   \n",
       "4                 [1, 2]            [1_1, 2_1]   \n",
       "..                   ...                   ...   \n",
       "2                 [1, 2]            [1_1, 2_1]   \n",
       "3              [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "4              [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "5              [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "6              [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "\n",
       "                                                  url  \n",
       "0   https://encode-public.s3.amazonaws.com/2020/11...  \n",
       "1   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "2   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "3   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "4   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "..                                                ...  \n",
       "2   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "3   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "4   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "5   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "6   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "\n",
       "[2419 rows x 26 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined = pd.concat(all_datasets)\n",
    "combined"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>organism</th>\n",
       "      <th>target</th>\n",
       "      <th>term_id</th>\n",
       "      <th>cell_line</th>\n",
       "      <th>institute_name</th>\n",
       "      <th>title</th>\n",
       "      <th>accession</th>\n",
       "      <th>status</th>\n",
       "      <th>assay_title</th>\n",
       "      <th>assay_term_name</th>\n",
       "      <th>...</th>\n",
       "      <th>output_category</th>\n",
       "      <th>output_type</th>\n",
       "      <th>read_length</th>\n",
       "      <th>read_length_units</th>\n",
       "      <th>run_type</th>\n",
       "      <th>schema_version</th>\n",
       "      <th>encode_version</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>technical_replicates</th>\n",
       "      <th>url</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>human</td>\n",
       "      <td>TCFL5</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF522WAN</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>human</td>\n",
       "      <td>ZNF75A</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF651OZY</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>human</td>\n",
       "      <td>ZBTB17</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF334KTM</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>human</td>\n",
       "      <td>TFE3</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF808TLR</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>human</td>\n",
       "      <td>ZNF586</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF977XAH</td>\n",
       "      <td>released</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>ChIP-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF831OKQ</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF872HBM</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF948GBJ</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>K562</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF450XLU</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>human</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>EFO:0001086</td>\n",
       "      <td>A549</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF225UNA</td>\n",
       "      <td>released</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>ATAC-seq</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2, 3]</td>\n",
       "      <td>[1_1, 2_1, 3_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2419 rows × 26 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   organism   target      term_id cell_line       institute_name  \\\n",
       "0     human    TCFL5  EFO:0002067      K562  Stanford University   \n",
       "1     human   ZNF75A  EFO:0002067      K562  Stanford University   \n",
       "2     human   ZBTB17  EFO:0002067      K562  Stanford University   \n",
       "3     human     TFE3  EFO:0002067      K562  Stanford University   \n",
       "4     human   ZNF586  EFO:0002067      K562  Stanford University   \n",
       "..      ...      ...          ...       ...                  ...   \n",
       "2     human  Unknown  EFO:0002067      K562  Stanford University   \n",
       "3     human  Unknown  EFO:0001187     HepG2  Stanford University   \n",
       "4     human  Unknown  EFO:0002784   GM12878  Stanford University   \n",
       "5     human  Unknown  EFO:0002067      K562  Stanford University   \n",
       "6     human  Unknown  EFO:0001086      A549  Stanford University   \n",
       "\n",
       "                       title    accession    status  assay_title  \\\n",
       "0   Michael Snyder, Stanford  ENCFF522WAN  released  TF ChIP-seq   \n",
       "1   Michael Snyder, Stanford  ENCFF651OZY  released  TF ChIP-seq   \n",
       "2   Michael Snyder, Stanford  ENCFF334KTM  released  TF ChIP-seq   \n",
       "3   Michael Snyder, Stanford  ENCFF808TLR  released  TF ChIP-seq   \n",
       "4   Michael Snyder, Stanford  ENCFF977XAH  released  TF ChIP-seq   \n",
       "..                       ...          ...       ...          ...   \n",
       "2   Michael Snyder, Stanford  ENCFF831OKQ  released     ATAC-seq   \n",
       "3   Michael Snyder, Stanford  ENCFF872HBM  released     ATAC-seq   \n",
       "4   Michael Snyder, Stanford  ENCFF948GBJ  released     ATAC-seq   \n",
       "5   Michael Snyder, Stanford  ENCFF450XLU  released     ATAC-seq   \n",
       "6   Michael Snyder, Stanford  ENCFF225UNA  released     ATAC-seq   \n",
       "\n",
       "   assay_term_name  ... output_category               output_type read_length  \\\n",
       "0         ChIP-seq  ...          signal  fold change over control         NaN   \n",
       "1         ChIP-seq  ...          signal  fold change over control         NaN   \n",
       "2         ChIP-seq  ...          signal  fold change over control         NaN   \n",
       "3         ChIP-seq  ...          signal  fold change over control         NaN   \n",
       "4         ChIP-seq  ...          signal  fold change over control         NaN   \n",
       "..             ...  ...             ...                       ...         ...   \n",
       "2         ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "3         ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "4         ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "5         ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "6         ATAC-seq  ...          signal  fold change over control         NaN   \n",
       "\n",
       "   read_length_units  run_type schema_version encode_version  \\\n",
       "0               None      None             26            4.0   \n",
       "1               None      None             26            4.0   \n",
       "2               None      None             26            4.0   \n",
       "3               None      None             26            4.0   \n",
       "4               None      None             26            4.0   \n",
       "..               ...       ...            ...            ...   \n",
       "2               None      None             26            4.0   \n",
       "3               None      None             26            4.0   \n",
       "4               None      None             26            4.0   \n",
       "5               None      None             26            4.0   \n",
       "6               None      None             26            4.0   \n",
       "\n",
       "   biological_replicates  technical_replicates  \\\n",
       "0                 [1, 2]            [1_1, 2_1]   \n",
       "1                 [1, 2]            [1_1, 2_1]   \n",
       "2                 [1, 2]            [1_1, 2_1]   \n",
       "3                 [1, 2]            [1_1, 2_1]   \n",
       "4                 [1, 2]            [1_1, 2_1]   \n",
       "..                   ...                   ...   \n",
       "2                 [1, 2]            [1_1, 2_1]   \n",
       "3              [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "4              [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "5              [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "6              [1, 2, 3]       [1_1, 2_1, 3_1]   \n",
       "\n",
       "                                                  url  \n",
       "0   https://encode-public.s3.amazonaws.com/2020/11...  \n",
       "1   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "2   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "3   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "4   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "..                                                ...  \n",
       "2   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "3   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "4   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "5   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "6   https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "\n",
       "[2419 rows x 26 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "combined"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Keeping only latest encode version of each file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "combined[\"string_biological_replicates\"] = combined[\"biological_replicates\"].astype(str)\n",
    "filtered_combined = combined.sort_values(\"encode_version\").groupby([\n",
    "    \"target\",\n",
    "    \"cell_line\",\n",
    "    \"assay_title\",\n",
    "    \"institute_name\",\n",
    "    \"string_biological_replicates\"\n",
    "]).last().reset_index()\n",
    "\n",
    "filtered_combined[\"url\"] = [\n",
    "    url.replace(\"private\", \"public\")\n",
    "    for url in filtered_combined.url\n",
    "]\n",
    "\n",
    "filtered_combined.to_csv(\"epigenomic_dataset/epigenomes_metadata/hg38.csv\", index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>target</th>\n",
       "      <th>cell_line</th>\n",
       "      <th>assay_title</th>\n",
       "      <th>institute_name</th>\n",
       "      <th>string_biological_replicates</th>\n",
       "      <th>organism</th>\n",
       "      <th>term_id</th>\n",
       "      <th>title</th>\n",
       "      <th>accession</th>\n",
       "      <th>status</th>\n",
       "      <th>...</th>\n",
       "      <th>output_category</th>\n",
       "      <th>output_type</th>\n",
       "      <th>read_length</th>\n",
       "      <th>read_length_units</th>\n",
       "      <th>run_type</th>\n",
       "      <th>schema_version</th>\n",
       "      <th>encode_version</th>\n",
       "      <th>biological_replicates</th>\n",
       "      <th>technical_replicates</th>\n",
       "      <th>url</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ADNP</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>human</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF290ZNR</td>\n",
       "      <td>released</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ADNP</td>\n",
       "      <td>K562</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>University of Chicago</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>human</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>Kevin White, UChicago</td>\n",
       "      <td>ENCFF340UTP</td>\n",
       "      <td>released</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2016/10...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AEBP2</td>\n",
       "      <td>HEK293</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>human</td>\n",
       "      <td>EFO:0001182</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF627OLR</td>\n",
       "      <td>released</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AFF1</td>\n",
       "      <td>K562</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>human</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF003ZRP</td>\n",
       "      <td>released</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/11...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AFF4</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>human</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF274ASN</td>\n",
       "      <td>released</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1724</th>\n",
       "      <td>ZXDB</td>\n",
       "      <td>HEK293</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>human</td>\n",
       "      <td>EFO:0001182</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF741ADU</td>\n",
       "      <td>released</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/08...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1725</th>\n",
       "      <td>ZXDC</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>human</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF805VXG</td>\n",
       "      <td>released</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/06...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1726</th>\n",
       "      <td>ZZZ3</td>\n",
       "      <td>GM12878</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>Harvard Medical School</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>human</td>\n",
       "      <td>EFO:0002784</td>\n",
       "      <td>Kevin Struhl, HMS</td>\n",
       "      <td>ENCFF636KMF</td>\n",
       "      <td>released</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>3.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2017/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1727</th>\n",
       "      <td>ZZZ3</td>\n",
       "      <td>HepG2</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>HudsonAlpha Institute for Biotechnology</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>human</td>\n",
       "      <td>EFO:0001187</td>\n",
       "      <td>Richard Myers, HAIB</td>\n",
       "      <td>ENCFF599UAF</td>\n",
       "      <td>released</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/07...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1728</th>\n",
       "      <td>ZZZ3</td>\n",
       "      <td>K562</td>\n",
       "      <td>TF ChIP-seq</td>\n",
       "      <td>Stanford University</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>human</td>\n",
       "      <td>EFO:0002067</td>\n",
       "      <td>Michael Snyder, Stanford</td>\n",
       "      <td>ENCFF481FFX</td>\n",
       "      <td>released</td>\n",
       "      <td>...</td>\n",
       "      <td>signal</td>\n",
       "      <td>fold change over control</td>\n",
       "      <td>NaN</td>\n",
       "      <td>None</td>\n",
       "      <td>None</td>\n",
       "      <td>26</td>\n",
       "      <td>4.0</td>\n",
       "      <td>[1, 2]</td>\n",
       "      <td>[1_1, 2_1]</td>\n",
       "      <td>https://encode-public.s3.amazonaws.com/2020/12...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1729 rows × 27 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     target cell_line  assay_title                           institute_name  \\\n",
       "0      ADNP     HepG2  TF ChIP-seq  HudsonAlpha Institute for Biotechnology   \n",
       "1      ADNP      K562  TF ChIP-seq                    University of Chicago   \n",
       "2     AEBP2    HEK293  TF ChIP-seq                      Stanford University   \n",
       "3      AFF1      K562  TF ChIP-seq                      Stanford University   \n",
       "4      AFF4     HepG2  TF ChIP-seq  HudsonAlpha Institute for Biotechnology   \n",
       "...     ...       ...          ...                                      ...   \n",
       "1724   ZXDB    HEK293  TF ChIP-seq                      Stanford University   \n",
       "1725   ZXDC     HepG2  TF ChIP-seq  HudsonAlpha Institute for Biotechnology   \n",
       "1726   ZZZ3   GM12878  TF ChIP-seq                   Harvard Medical School   \n",
       "1727   ZZZ3     HepG2  TF ChIP-seq  HudsonAlpha Institute for Biotechnology   \n",
       "1728   ZZZ3      K562  TF ChIP-seq                      Stanford University   \n",
       "\n",
       "     string_biological_replicates organism      term_id  \\\n",
       "0                          [1, 2]    human  EFO:0001187   \n",
       "1                          [1, 2]    human  EFO:0002067   \n",
       "2                          [1, 2]    human  EFO:0001182   \n",
       "3                          [1, 2]    human  EFO:0002067   \n",
       "4                          [1, 2]    human  EFO:0001187   \n",
       "...                           ...      ...          ...   \n",
       "1724                       [1, 2]    human  EFO:0001182   \n",
       "1725                       [1, 2]    human  EFO:0001187   \n",
       "1726                       [1, 2]    human  EFO:0002784   \n",
       "1727                       [1, 2]    human  EFO:0001187   \n",
       "1728                       [1, 2]    human  EFO:0002067   \n",
       "\n",
       "                         title    accession    status  ... output_category  \\\n",
       "0          Richard Myers, HAIB  ENCFF290ZNR  released  ...          signal   \n",
       "1        Kevin White, UChicago  ENCFF340UTP  released  ...          signal   \n",
       "2     Michael Snyder, Stanford  ENCFF627OLR  released  ...          signal   \n",
       "3     Michael Snyder, Stanford  ENCFF003ZRP  released  ...          signal   \n",
       "4          Richard Myers, HAIB  ENCFF274ASN  released  ...          signal   \n",
       "...                        ...          ...       ...  ...             ...   \n",
       "1724  Michael Snyder, Stanford  ENCFF741ADU  released  ...          signal   \n",
       "1725       Richard Myers, HAIB  ENCFF805VXG  released  ...          signal   \n",
       "1726         Kevin Struhl, HMS  ENCFF636KMF  released  ...          signal   \n",
       "1727       Richard Myers, HAIB  ENCFF599UAF  released  ...          signal   \n",
       "1728  Michael Snyder, Stanford  ENCFF481FFX  released  ...          signal   \n",
       "\n",
       "                   output_type read_length read_length_units run_type  \\\n",
       "0     fold change over control         NaN              None     None   \n",
       "1     fold change over control         NaN              None     None   \n",
       "2     fold change over control         NaN              None     None   \n",
       "3     fold change over control         NaN              None     None   \n",
       "4     fold change over control         NaN              None     None   \n",
       "...                        ...         ...               ...      ...   \n",
       "1724  fold change over control         NaN              None     None   \n",
       "1725  fold change over control         NaN              None     None   \n",
       "1726  fold change over control         NaN              None     None   \n",
       "1727  fold change over control         NaN              None     None   \n",
       "1728  fold change over control         NaN              None     None   \n",
       "\n",
       "      schema_version encode_version biological_replicates  \\\n",
       "0                 26            4.0                [1, 2]   \n",
       "1                 26            3.0                [1, 2]   \n",
       "2                 26            4.0                [1, 2]   \n",
       "3                 26            4.0                [1, 2]   \n",
       "4                 26            4.0                [1, 2]   \n",
       "...              ...            ...                   ...   \n",
       "1724              26            4.0                [1, 2]   \n",
       "1725              26            4.0                [1, 2]   \n",
       "1726              26            3.0                [1, 2]   \n",
       "1727              26            4.0                [1, 2]   \n",
       "1728              26            4.0                [1, 2]   \n",
       "\n",
       "     technical_replicates                                                url  \n",
       "0              [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "1              [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2016/10...  \n",
       "2              [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/08...  \n",
       "3              [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/11...  \n",
       "4              [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "...                   ...                                                ...  \n",
       "1724           [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/08...  \n",
       "1725           [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/06...  \n",
       "1726           [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2017/07...  \n",
       "1727           [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/07...  \n",
       "1728           [1_1, 2_1]  https://encode-public.s3.amazonaws.com/2020/12...  \n",
       "\n",
       "[1729 rows x 27 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filtered_combined"
   ]
  }
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