boulardlab/ogt_mouse_models_formichetti2024

All custom code for RNA-Seq analyses in Ogt's mouse alleles paper (Formichetti et al., 2024). Outputs (containing raw version of paper figures) at link below.

Formichetti et al., 2024 - A murine allelic series of Ogt catalytic hypomorphic mutants uncovers the requirement of O-GlcNAc for embryonic development

Introduction

• This repository contains all code used to generate the figures and conclusions based on RNA-Seq data contained in paper "A murine allelic series of Ogt catalytic hypomorphic mutants uncovers the requirement of O-GlcNAc for embryonic development" ([Formichetti et al. 2024](link to biorxiv to add)).

• For each sequencing dataset, there is a subrepository with a self-explanatory name.

General overview of the workflows

Analysis of single copy genes

1. a Galaxy pipeline starting from fastq files to read counts, found in src/galaxy: which outputs:

• transcripts counts in the case of MEFs and placentae, summarized at gene level downstream in Rmd
• gene counts in the case of single blastocysts

2. different kinds of custom downstream analyses using the output of the pipeline and performed with R, all included in Rmd files with self-explanatory names, found in src/Rmd and whose output is here. Order for running the Rmd, if more than one and if not obvious, is specified in the main README of each subdirectory.

Analysis of retrotransposons' expression

1. a custom snakemake pipeline, found in snake-make/TE_RNASeq.Snakefile of each subrepository. Config files for the pipeline are in config/ and conda environments are in env/conda

2. custom downstream analyses using the output of the pipeline and performed with R, all included in src/Rmd/TE_analysis.Rmd and whose output is here.

Raw data

Sequencing data generated in our study are available at:

• E-MTAB-13499: “Smart-Seq of female and male blastocysts from mothers bearing the OgtT931A and OgtT931del mutations”
• E-MTAB-13299: "mRNA-Seq of placentas bearing the OgtY851A mutation"
• E-MTAB-13297: "SMART-Seq of untreated and auxin-treated blastocysts for OGT degradation"
• E-MTAB-13298: "mRNA-Seq of primary MEFs untreated or treated with auxin for OGT degradation"