GEO series

FACT orchestrates the interplay between chromatin structure and transcription [ChIP-Seq]

GSE242372 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 16 samples Submitted 2024/05/30 Platform GPL21697

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 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: 16 samples: 16 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: FACT maintains chromatin architecture and thereby stimulates RNA polymerase II pausing during transcription in vivoMolecular cell · 2024

Summary (written by the submitters)

Transcription by RNA polymerase II (RNA Pol II) depends on transcription factors and chromatin factors. Here we use rapid factor depletion and multiomics analysis to investigate how a histone chaperone, FAcilitates Chromatin Transcription (FACT), influence nascent transcription by RNA PolII in human cells. Depletion of a FACT subunit, SSRP1, led to rapid changes in chromatin structure and concomitantly strongly compromised RNA synthesis.

Read the full summary ↓

FACT depletion led to a multilayered transcriptional defect, including loss of promoter proximal pausing, deregulated release into elongation and drop-off of RNA Pol II in promoter-distant gene regions. We combined these analyses with biochemical dissection of transcription of a chromatinized template to show that FACT supports both elongation and pausing of RNA Pol II. Our study also provides new evidence how the position of promoter proximal pausing is defined by the +1 nucleosome in human cells.

Published in

FACT maintains chromatin architecture and thereby stimulates RNA polymerase II pausing during transcription in vivo

Žumer K, Ochmann M, Aljahani A et al. · Molecular cell 2024 · PMID 38810649 · doi:10.1016/j.molcel.2024.05.003

This dataset

Open GSE242372 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 GSE242372_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 PRJNA1041364 and SRA study SRP473299. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38810649) ↗

Study design

16 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 16 sample titles: 16 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

GSM7761853 K562, SSRP1-dTAG, Pol II, ChIP, DMSO, rep1, 1h
GSM7761854 K562, SSRP1-dTAG, Pol II, ChIP, dTAG7, rep1, 1h
GSM7761855 K562, SSRP1-dTAG, Pol II, ChIP, DMSO, rep2, 1h
GSM7761856 K562, SSRP1-dTAG, Pol II, ChIP, dTAG7, rep2, 1h
GSM7761857 K562, SSRP1-dTAG, Pol II, ChIP, DMSO, rep1, 4h
GSM7761858 K562, SSRP1-dTAG, Pol II, ChIP, dTAG7, rep1, 4h
GSM7761859 K562, SSRP1-dTAG, Pol II, ChIP, DMSO, rep2, 4h
GSM7761860 K562, SSRP1-dTAG, Pol II, ChIP, dTAG7, rep2, 4h
GSM7761861 K562, SSRP1-dTAG, NELF (Th1L), ChIP, DMSO, rep1, 1h
GSM7761862 K562, SSRP1-dTAG, NELF (Th1L), ChIP, dTAG7, rep1, 1h
GSM7761863 K562, SSRP1-dTAG, NELF (Th1L), ChIP, DMSO, rep2, 1h
GSM7761864 K562, SSRP1-dTAG, NELF (Th1L), ChIP, dTAG7, rep2, 1h
GSM7761865 K562, SSRP1-dTAG, NELF (Th1L), ChIP, DMSO, rep1, 4h
GSM7761866 K562, SSRP1-dTAG, NELF (Th1L), ChIP, dTAG7, rep1, 4h
GSM7761867 K562, SSRP1-dTAG, NELF (Th1L), ChIP, DMSO, rep2, 4h
GSM7761868 K562, SSRP1-dTAG, NELF (Th1L), ChIP, dTAG7, rep2, 4h

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Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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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.