This is the repository which contains the code that was used to generate the results and figures for the manuscript "Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development" (https://www.biorxiv.org/content/10.1101/2023.03.20.533545v1.full).
The data is also available to navigate at our web portal Daniocell: https://daniocell.nichd.nih.gov/
This data was used to search for gene expression programs that are reused across multiple tissues, to determine the duration of transcriptional states during development, and identify dividing populations that are present for long developmental durations. Since global analysis of a dataset of this complexity rarely reveals its full cellular diversity, focused analyses was also performed within selected tissues - the non-skeletal muscle and the endoderm.
The code is organized into individual folders and numbered in the order they were used to generate the figures in the manuscript. Below is a description of which folders contain the code used to generate the different figure panels in the manuscript.
I. 01_Pre-processing: contains the code used to combine the previously published (Farrell et al., 2018) dataset (3.3-12 hpf) and the newly generated dataset (14-120 hpf).
II. 02_Clustering: contains the code used to generate figure panels Figure 1B, C, and Figure S1A, H.
III. 03_Gene stats: contains the code used to generate figure panels Figure 1D–F, Figure S1I–K.
IV. 04_Persistent: contains the code used to generate the figure panels Figure 2, Figure S2.
V. 05_Gene_Modules: contains the code that was used to generate the figure panels Figure 3A-D and Figure S3A-B
VI. 06_Smooth_Muscle: contains the code that was used to generate the figure panels Figure 4A-D, I, M; Figure 5A-B, H, I; Figure S4A-C; Figure S5A-C; Figure S6I, J, K; Figure S7
VII. 07_Intestine: contains the code that was used to generate the figure panels Figure 6A-C, F-G, Figure 7A-F, I; Figure S8A-B, Figure S9, Figure S10.
The raw sequencing reads in FASTQ format can be obtained from NCBI GEO GSE223922.
A UMI counts table containing all cells can also be obtained from NCBI GEO GSE223922.