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Genome-wide interference of chromatin architecture and Mediator in transcriptional bursting and gene network regulation

GSE241338 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 250 samples Submitted 2024/06/30 Platform GPL21493Platform GPL24676Platform GPL21697Platform GPL21290Platform GPL24247Platform GPL30173Platform GPL34284Platform GPL16791
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 250 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
250 samples: 207 distinct titles, 39 of them repeatedGroups 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
3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene networkScience advances · 2024
Summary (written by the submitters)
Gene expression is a stochastic process that occurs in bursts of RNA synthesis. We applied a mathematical model to scRNA-Seq data to infer bursting dynamics transcriptome-wide under multiple perturbations in a wide range of cell types and identified possible molecular mechanisms. We find that mediator complex subunit MED26 primarily regulates frequency, MYC regulates burst size, while cohesin and super-enhancers can modulate both.
Read the full summary ↓
Despite comparable effect sizes on RNA levels amongst these perturbations, we find that acute depletion of MED26 plays a larger role in perturbing gene regulatory networks. Furthermore, this perturbation acts downstream of both chromatin spatial architecture and preinitiation complex formation, indicating that later steps in the initiation of transcriptional bursts are primary nodes for integrating gene networks in single cells.
Published in
3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network
Trzaskoma P, Jung S, Pękowska A et al. · Science advances 2024 · PMID 39121214 · doi:10.1126/sciadv.adl4893
This dataset
Open GSE241338 in finder → Find more 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 GSE241338_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 PRJNA1007704 and SRA study SRP456201. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39121214) ↗
Study design
207 distinct titles, 39 of them repeated
HCTJQ_mRNA_DMSO ×3 HCTJQ_mRNA_JQ1 ×3 HCTMED26D_mRNA_AUXIN ×3 HCTMED26D_mRNA_DMSO ×3 scRNA_HCT_DMSO ×2 scRNA_HCTJQ1_DMSO ×2 scRNA_HCTJQ1_JQ1 ×2 scRNA_HCTMED26D_DMSO ×2 +31 more

How we read this: Read from 250 sample titles: 207 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

+ 210 more — browse all 250 samples with per-sample file links →

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.