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Chromatin reorganization drives expression of functional maturation genes in senescent pancreatic beta cells (Series3 - Chromatin profiles, ChIP-seq)

GSE207822 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 40 samples Submitted 2024/06/26 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 40 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
Homo sapiens (human)
Samples
40 samples: 16 conditions, mostly in triplicateGroups 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
Senescence of human pancreatic beta cells enhances functional maturation through chromatin reorganization and promotes interferon responsivenessNucleic acids research · 2024
Summary (written by the submitters)
Using a unique model of cultured human beta cell senescence we show that chromatin reorganization leads to activation of enhancers regulating functional maturation genes, concomitantly with acquisition of glucose-stimulated insulin secretion capacity. Interferon-response genes are elevated in senescent beta cells, but cytokine-encoding senescence-associated secretory phenotype (SASP) genes are not.
Read the full summary ↓
Human beta cell senescence thus involves chromatin-driven upregulation of a functional maturation program and of interferon-stimulated genes, changes that could increase both insulin secretion and immune reactivity.
Published in
Senescence of human pancreatic beta cells enhances functional maturation through chromatin reorganization and promotes interferon responsiveness
Patra M, Klochendler A, Condiotti R et al. · Nucleic acids research 2024 · PMID 38682582 · doi:10.1093/nar/gkae313
This dataset
Open GSE207822 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE207822_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 PRJNA857288 and SRA study SRP385695. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38682582) ↗
Study design
16 conditions, mostly in triplicate
EndoC-βH3 cells, Non senescent cells, H3K27ac ×3 EndoC-βH3 cells, Senescent cells, H3K27ac ×3 EndoC-βH3 cells, Non senescent cells, Input o… ×3 EndoC-βH3 cells, Senescent cells, Input of H3… ×3 EndoC-βH3 cells, Non senescent cells, CTCF ×3 EndoC-βH3 cells, Senescent cells, CTCF ×3 EndoC-βH3 cells, Non senescent cells, Input o… ×3 EndoC-βH3 cells, Senescent cells, Input of CT… ×3 +8 more

Supports a between-group comparison across 40 samples.

How we read this: 16 replicated groups read from 40 sample titles; they account for 40 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
Datasets on a similar topic

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