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Metabolic adaptation pilots the differentiation of human hematopoietic cells (bulk ATAC-Seq)

GSE243003 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 41 samples Submitted 2024/05/22 Platform GPL15520Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 41 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
41 samples: 13 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
Metabolic adaptation pilots the differentiation of human hematopoietic cellsLife science alliance · 2024
Summary (written by the submitters)
In order to get insight in the role of metabolic perturbations during the first steps of cell differentiation, the phenotype, gene expression profile and chromatin accessibility of CD34+ cells were examined using bulk- and single-cell techniques during the initial 96 hours of in vitro differentiation. Specific enzyme inhibitors targeting key steps of the energy metabolism were employed to induce perturbations and assess their effect.
Read the full summary ↓
The results support a model whereby energy requirements play the role of initiator of differentiation. According to it, metabolic perturbations induce rapid and non-specific, enabling a state of multi-primed gene expression. A selective re-compaction of the chromatin constrained by the availability of key metabolites essential for repressive epigenetic modifications and by the action of transcription regulator proteins consolidates the phenotypic response of the cells.
Published in
Metabolic adaptation pilots the differentiation of human hematopoietic cells
Racine L, Parmentier R, Niphadkar S et al. · Life science alliance 2024 · PMID 38802246 · doi:10.26508/lsa.202402747
This dataset
Open GSE243003 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 GSE243003_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 PRJNA1015714 and SRA study SRP460005. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38802246) ↗
Study design
13 conditions, mostly in triplicate
bulkATACseq_CD34+_CTRL_24h ×5 bulkATACseq_CD34+_Xvivo_00h ×3 bulkATACseq_CD34+_CTRL_03h ×3 bulkATACseq_CD34+_CTRL_12h ×3 bulkATACseq_CD34+_2DG_03h ×3 bulkATACseq_CD34+_2DG_12h ×3 bulkATACseq_CD34+_2DG_24h ×3 bulkATACseq_CD34+_DON_03h ×3 +5 more

Supports a between-group comparison across 41 samples.

How we read this: 13 replicated groups read from 41 sample titles; they account for 41 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

+ 1 more — browse all 41 samples with per-sample file links →

Datasets on a similar topic

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