Welcome to the code repository for Hochbaum et al., 2024

MoSeq

The notebook used to generate panels and statistics related to the MoSeq experiment in $Figure S3$ is located in 'MoSeq_figS3'

MoSeq data:

The MoSeq related dataframes are located within: https://dataverse.harvard.edu/dataverse/2024_hochbaum_thyroid

Reinforcement learning modeling (Q-learning) for 2ABT

To install the Q-learning model for the 2-arm bandit analysis, install the package contained within the Q_learning_2ABT subfolder. Instructions: Open a terminal and navigate to the 'Q_learning_2ABT' sub-directory

cd Q_learning_2ABT

Install the package

pip install .

2ABT modeling notebook:

The notebook used to run Q-learning models is located in '2ABT_run_Qlearning'

2ABT data:

Mouse 2ABT dataframes used for Q-learning modeling and analyses in $Figures 5/6/S6$ are located within: https://dataverse.harvard.edu/dataverse/2024_hochbaum_thyroid

snRNA-seq

Scripts for processing, annotating, and analyzing the single-nucleus RNA sequencing experiments (Figures 2, 3, S4). Raw and filtered data are publicly available as of date of publication on an NCBI GEO data repository (GSE271421) and CELLxGENE repository (https://cellxgene.cziscience.com/collections/c450e15d-321a-42d6-986b-11409d04896d).

00_scOnline_sourceCode

Source code utilized from Gazestani, V., Kamath, T., Nadaf, N.M., Dougalis, A., Burris, S.J., Rooney, B., Junkkari, A., Vanderburg, C., Pelkonen, A., Gomez-Budia, M., et al. (2023). Early Alzheimer’s disease pathology in human cortex involves transient cell states. Cell 186, 4438–4453.e23. https://doi.org/10.1016/j.cell.2023.08.005.

01_seuratProcessing

Scripts for initial processing of filtered feature barcode matrix data and major cell class annotation.

02_labelTransfer

Example scripts for neuronal and non-neuronal subtype annotation based on published mouse motor cortex reference dataset (Yao, Z., Liu, H., Xie, F., Fischer, S., Adkins, R.S., Aldridge, A.I., Ament, S.A., Bartlett, A., Behrens, M.M., Van den Berge, K., et al. (2021). A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 598, 103–110. https://doi.org/10.1038/s41586-021-03500-8).

03_differentialExpression

Example scripts for the T3 vs. C differential expression (DE) analysis in control animals (Figure 2) and Cre+ vs. Cre- DE analysis in T3+ DN-THR or WT-THR animals (Figure 3).

04_analyses

Downstream analyses (i.e. ordered gene set enrichment analysis) performed on DE results.