GEO series

Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity.

GSE276572 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2024/09/12 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 12 samples: 6 conditions, mostly in duplicateGroups 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.

Summary (written by the submitters)

Caloric restriction (CR) extends organismal life- and health-span by improving glucose homeostasis. How CR affect the structure-function of pancreatic beta cells remains unknown. We used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis.

Read the full summary ↓

Gene regulatory network analysis reveal that CR activates transcription factors important for beta cell identity and homeostasis, while imaging metabolomics demonstrates that CR beta cells are more energetically competent. In fact, high-resolution microscopy show that CR reduces beta cell mitophagy to increase mitochondria mass and the potential for ATP generation. However, CR beta cells have impaired adaptive pro liferation in response to high fat diet feeding. Finally, we show that long-term CR delays the onset of beta cell aging and promotes cell longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cell structure-function during aging and diabetes. 27 diabetes.

This dataset

Open GSE276572 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 GSE276572_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1157864 and SRA study SRP531199. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in duplicate

HF, ATAC, islets, ×2 HF, GEX, islets, ×2 AL, ATAC, islets, ×2 AL, GEX, islets, ×2 CR, ATAC, islets, ×2 CR, GEX, islets, ×2

Supports a between-group comparison across 12 samples.

How we read this: 6 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

GSM8502269 HF, ATAC, islets, rep1 HF, ATAC, islets,
GSM8502270 HF, GEX, islets, rep1 HF, GEX, islets,
GSM8502271 AL, ATAC, islets, rep1 AL, ATAC, islets,
GSM8502272 AL, GEX, islets, rep1 AL, GEX, islets,
GSM8502273 CR, ATAC, islets, rep1 CR, ATAC, islets,
GSM8502274 CR, GEX, islets, rep1 CR, GEX, islets,
GSM8502275 AL, ATAC, islets, rep2 AL, ATAC, islets,
GSM8502276 AL, GEX, islets, rep2 AL, GEX, islets,
GSM8502277 CR, ATAC, islets, rep2 CR, ATAC, islets,
GSM8502278 CR, GEX, islets, rep2 CR, GEX, islets,
GSM8502279 HF, ATAC, islets, rep2 HF, ATAC, islets,
GSM8502280 HF, GEX, islets, rep2 HF, GEX, islets,

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.