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The Swi/Snf chromatin remodeling complex regulates pancreatic endocrine cell expansion and differentiation in vivo

GSE248369 Mus musculus (mouse) Single-cell RNA-seq 10 samples Submitted 2024/05/31 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 10 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
10 samples: 4 × Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-dEndo vs 3 × Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-Control vs 3 × Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-DKOGroups 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
The SWI/SNF chromatin remodelling complex regulates pancreatic endocrine cell expansion and differentiation in mice in vivoDiabetologia · 2024
Summary (written by the submitters)
Strategies to augment functional β-cell mass include directed differentiation of stem cells towards a β-cell fate, which requires extensive knowledge of transcriptional programs governing endocrine progenitor cell differentiation in vivo. Here we describe the contributions of the Brg1 and Brm ATPase subunits of the Swi/Snf chromatin remodeling complex on endocrine cell development.
Read the full summary ↓
Through the use of transgenic knockout animal models we reveal that conditional knockout of Brg1 in endocrine progenitors results in blood glucose dysregulation, reduced islet mass and function, while loss of all Swi/Snf activity (Brg1 and Brm) results in early postnatal death, resulting from severe hyperglycemia and reduced β-cell mass. Single-cell RNA Sequencing of embryonic day 15.5 lineage-labeled cells revealed reduced expression of maturation markers, proliferation genes, and hormones in endocrine-committed, β- and α-cell clusters, highlighting a critical role for Swi/Snf in governing gene-expression programs essential for endocrine cell development.
Published in
The SWI/SNF chromatin remodelling complex regulates pancreatic endocrine cell expansion and differentiation in mice in vivo
Davidson RK, Wu W, Kanojia S et al. · Diabetologia 2024 · PMID 38958700 · doi:10.1007/s00125-024-06211-7
This dataset
Open GSE248369 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 GSE248369_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1043613 and SRA study SRP473253. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38958700) ↗
Study design
4 × Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-dEndo vs 3 × Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-Control vs 3 × Flow-Sorted e15.5 endocrine-committed and endocrine-progenitor cells-DKO

Supports a between-group comparison across 10 samples.

How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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
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