GEO series

CHD7 and SOX2 Act in a Common Gene Regulatory Network During Mammalian Semicircular Canal and Cochlear Development (RNA-Seq)

GSE239361 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/03/01 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 12 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 12 samples: 3 × E10.5 otocyst wild type vs 3 × E10.5 otocyst Sox2CreER/+ vs 3 × E10.5 otocyst Chd7Gt/+ vs 3 × E10.5 otocyst Chd7Gt/+;Sox2CreER/+Groups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: CHD7 and SOX2 act in a common gene regulatory network during mammalian semicircular canal and cochlear developmentProceedings of the National Academy of Sciences of the United States of America · 2024

Summary (written by the submitters)

Inner ear morphogenesis requires tightly regulated epigenetic and transcriptional control of gene expression. CHD7, an ATP-dependent chromodomain helicase DNA-binding protein, and SOX2, an SRY-related HMG box pioneer transcription factor, are known to contribute to vestibular and auditory system development, but their genetic interactions in the ear have not been explored.

Read the full summary ↓

Here, we analyzed inner ear development and the transcriptional regulatory landscapes in mice with variable dosage of Chd7 and/or Sox2. We show that combined haploinsufficiency for Chd7 and Sox2 results in reduced otic cell proliferation, severe malformations of semicircular canals, and shortened cochlea with ectopic hair cells. Examination of mice with conditional, inducible Chd7 loss by Sox2CreER reveals a critical period (~E9.5) of susceptibility in the inner ear to combined Chd7 and Sox2 loss. Data from genome-wide RNA-sequencing and CUT&Tag studies in the otocyst show that CHD7 regulates Sox2 expression and acts early in a gene regulatory network to control expression of key otic patterning genes, including Pax2 and Otx2. CHD7 and SOX2 directly bind independently and cooperatively at transcription start sites and enhancers to regulate otic progenitor cell proliferation and function. Together, our findings reveal essential roles for Chd7 and Sox2 in the early inner ear and may be applicable for CHD7 and SOX2 related syndromic and other forms of hearing or balance disorders.

Published in

CHD7 and SOX2 act in a common gene regulatory network during mammalian semicircular canal and cochlear development

Gao J, Skidmore JM, Cimerman J et al. · Proceedings of the National Academy of Sciences of the United States of America 2024 · PMID 38408234 · doi:10.1073/pnas.2311720121

This dataset

Open GSE239361 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE239361_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA998900 and SRA study SRP451615. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38408234) ↗

Study design

3 × E10.5 otocyst wild type vs 3 × E10.5 otocyst Sox2CreER/+ vs 3 × E10.5 otocyst Chd7Gt/+ vs 3 × E10.5 otocyst Chd7Gt/+;Sox2CreER/+

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM7663604 E10.5 otocyst wild type replicate 1 E10.5 otocyst wild type
GSM7663605 E10.5 otocyst Sox2CreER/+ replicate 1 E10.5 otocyst Sox2CreER…
GSM7663606 E10.5 otocyst Chd7Gt/+ replicate 1 E10.5 otocyst Chd7Gt/+
GSM7663607 E10.5 otocyst Chd7Gt/+;Sox2CreER/+ replicate 1 E10.5 otocyst Chd7Gt/+;…
GSM7663608 E10.5 otocyst wild type replicate 2 E10.5 otocyst wild type
GSM7663609 E10.5 otocyst Sox2CreER/+ replicate 2 E10.5 otocyst Sox2CreER…
GSM7663610 E10.5 otocyst Chd7Gt/+ replicate 2 E10.5 otocyst Chd7Gt/+
GSM7663611 E10.5 otocyst Chd7Gt/+;Sox2CreER/+ replicate 2 E10.5 otocyst Chd7Gt/+;…
GSM7663612 E10.5 otocyst wild type replicate 3 E10.5 otocyst wild type
GSM7663613 E10.5 otocyst Sox2CreER/+ replicate 3 E10.5 otocyst Sox2CreER…
GSM7663614 E10.5 otocyst Chd7Gt/+ replicate 3 E10.5 otocyst Chd7Gt/+
GSM7663615 E10.5 otocyst Chd7Gt/+;Sox2CreER/+ replicate 3 E10.5 otocyst Chd7Gt/+;…

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