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PGE2 alters chromatin through H2A.Zvariant enhancer nucleosome modification to promote hematopoietic stem cell fate (ChIP-Seq)

GSE229396 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 26 samples Submitted 2024/06/10 Platform GPL16791Platform GPL20301
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 26 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
26 samples: 26 samples, each with a distinct title — no replicated groupsGroups 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
PGE(2) alters chromatin through H2A.Z-variant enhancer nucleosome modification to promote hematopoietic stem cell fateProceedings of the National Academy of Sciences of the United States of America · 2023
Summary (written by the submitters)
Hematopoietic stem and progenitor cells (HSPCs) need require tight transcriptional regulation. In-depth knowledge on how epigenetic mechanisms regulate chromatin landscape in order to control gene expression, particularly in response to external stimuli, will be key to understand the pathogenesis of hematologic disorders and improve blood stem cell-based therapies.
Read the full summary ↓
Prostaglandin E2 (PGE2) and its metabolically resistant analog 16,16-dimethyl-PGE2 (dmPGE2) were previously identified as a potent external stimulus to enhance HSPC engraftment. PGE2 has been evaluated in various clinical trials to improve engraftment of stem cells. To understand the mechanism of gene expression changes, Wwe identified that dmPGE2 mediates chromatin flexibility at HSPC-specific enhancers through histone-variant H2A.Z acetylation to promote master transcription factor (TF) binding and reinforce expression of genes involved in stem cell fate and engraftment.
Published in
PGE(2) alters chromatin through H2A.Z-variant enhancer nucleosome modification to promote hematopoietic stem cell fate
Sporrij A, Choudhuri A, Prasad M et al. · Proceedings of the National Academy of Sciences of the United States of America 2023 · PMID 37126722 · doi:10.1073/pnas.2220613120
This dataset
Open GSE229396 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 GSE229396_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 PRJNA954360 and SRA study SRP432038. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37126722) ↗
Study design
26 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 26 sample titles: 26 distinct titles with little repetition. 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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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.