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Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (ChIP-Seq)

GSE241924 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 45 samples Submitted 2024/03/06 Platform GPL21697
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 45 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)
Topic
Gastrointestinal stromal tumourThis series is part of our curated briefing on it.
Samples
45 samples: 22 conditions, mostly in duplicateGroups 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.
Summary (written by the submitters)
Enhancer-Promoter communication is dependent on the topological organization of genomic DNA, including topologically-associated domains (TADs) and boundaries enforced by the CTCF insulator protein. Here, we characterized the structure and function of the FGF3/4 locus and the boundary element that insulates the region from an enhancer in the adjacent TAD.
This dataset
Open GSE241924 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Gastrointestinal stromal tumour landscape →
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 GSE241924_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 PRJNA1010763 and SRA study SRP457559. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
22 conditions, mostly in duplicate
GIST-T1, control, CTCF, ×2 GIST-T1, InsE, CTCF, ×2 GIST-T1, InsF, CTCF, ×2 GIST-T1, InsG, CTCF, ×2 GIST-T1, InsH, CTCF, ×2 GIST-T1, control, H3K27ac, ×2 GIST-T1, InsE, H3K27ac, ×2 GIST-T1, InsF, H3K27ac, ×2 +15 more

Supports a between-group comparison across 44 samples.

How we read this: 22 replicated groups read from 45 sample titles; they account for 44 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

+ 5 more — browse all 45 samples with per-sample file links →

More Gastrointestinal stromal tumour datasets

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

Share this dataset

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.