Sidy2015 / somitogenesis2022

Code related to the mouse somitogenesis project

A transcriptional and regulatory map of mouse somitogenesis

This repository contains the code related to the publication A transcriptional and regulatory map of mouse somitogenesis (Ibarra-Soria, Thierion et al., 2023).

Data

The raw and processed data from this study are available in the ArrayExpress repository and can be accessed through the BioStudies database (https://www.ebi.ac.uk/biostudies/):

• RNA-seq dataset: E-MTAB-12511.
• ATAC-seq dataset: E-MTAB-12539.

These include the raw FASTQ files as well as gene/peak count tables provided as processed data.

Code

All code used to pre-process and analyse the data is provided, in the scripts directories within each of the data modality folders.

• RNA-seq and ATAC-seq directories contain the primary analysis of each data type.
• RNA+ATAC directory contains analyses that integrate both information sources.

Results

RNA-seq/results contains all differential expression results (between somite trios and across developmental stages).

ATAC-seq/results contains all differential accessibility results (between somite trios and across developmental stages).