GEO series

CTCF distribution around AsisI sites in IDHwt and IDHR132H DIvA cells

GSE283196 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 117 samples Submitted 2025/02/12 Platform GPL24676Platform GPL30173

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 117 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: 117 samples: 51 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.
Paper: D-2-hydroxyglutarate impairs DNA repair through epigenetic reprogrammingNature communications · 2025

Summary (written by the submitters)

IDH1 mutation impacts CTCF binding and function through methylating cytosine in the CTCF binding motif. We hypothesize that the impairment of CTCF-associated DNA repair process may be relevant to the loss of CTCF chromatin association and shifts in chromatin conformation. Chromatin immunoprecipitation-sequencing confirmed the loss of CTCF coverage in the proximity sites of AsisI sites in IDH1 mutant cells.

Published in

D-2-hydroxyglutarate impairs DNA repair through epigenetic reprogramming

Lang F, Kaur K, Fu H et al. · Nature communications 2025 · PMID 39920158 · doi:10.1038/s41467-025-56781-2

This dataset

Open GSE283196 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 GSE283196_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 PRJNA1193016 and SRA study SRP548668. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39920158) ↗

Study design

51 conditions, mostly in duplicate

DIvA cell, IDH wt, non treated, CTCF, ChIP, ×4 DIvA cell, IDH wt, 4-OHT, CTCF, ×4 DIvA cell, IDH mutant, non treated, CTCF, ×4 DIvA cell, IDH mutant, 4-OHT,CTCF, ×4 DIvA cell, IDH wt, non treated, input, ×4 DIvA cell, IDH wt, 4-OHT, input, ×4 DIvA cell, IDH mutant, non treated, TETdCD, ×3 DIvA cell, IDH mutant, non treated, TETCD, ×2 +45 more

Supports a case/control comparison: 77 samples read as cases, 20 as controls.

How we read this: 51 replicated groups read from 117 sample titles; they account for 115 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

GSM8657501 DIvA cell, IDH wt, non treated, CTCF, ChIP, Rep 1 DIvA cell, IDH wt, non …
GSM8657502 DIvA cell, IDH wt, non treated, CTCF, ChIP, Rep 2 DIvA cell, IDH wt, non …
GSM8657503 DIvA cell, IDH wt, non treated, CTCF, ChIP, Rep 3 DIvA cell, IDH wt, non …
GSM8657504 DIvA cell, IDH wt, non treated, CTCF, ChIP, Rep 4 DIvA cell, IDH wt, non …
GSM8657506 DIvA cell, IDH wt, 4-OHT, CTCF, Rep 1 DIvA cell, IDH wt, 4-OH…
GSM8657507 DIvA cell, IDH wt, 4-OHT, CTCF, Rep 2 DIvA cell, IDH wt, 4-OH…
GSM8657508 DIvA cell, IDH wt, 4-OHT, CTCF, Rep 3 DIvA cell, IDH wt, 4-OH…
GSM8657509 DIvA cell, IDH wt, 4-OHT, CTCF, Rep 4 DIvA cell, IDH wt, 4-OH…
GSM8657510 DIvA cell, IDH mutant, non treated, CTCF, Rep 1 DIvA cell, IDH mutant, …
GSM8657511 DIvA cell, IDH mutant, non treated, CTCF, Rep 2 DIvA cell, IDH mutant, …
GSM8657512 DIvA cell, IDH mutant, non treated, CTCF, Rep 3 DIvA cell, IDH mutant, …
GSM8657513 DIvA cell, IDH mutant, non treated, CTCF, Rep 4 DIvA cell, IDH mutant, …
GSM8657514 DIvA cell, IDH mutant, 4-OHT,CTCF, Rep 1 DIvA cell, IDH mutant, …
GSM8657515 DIvA cell, IDH mutant, 4-OHT,CTCF, Rep 2 DIvA cell, IDH mutant, …
GSM8657516 DIvA cell, IDH mutant, 4-OHT,CTCF, Rep 3 DIvA cell, IDH mutant, …
GSM8657517 DIvA cell, IDH mutant, 4-OHT,CTCF, Rep 4 DIvA cell, IDH mutant, …
GSM8657518 DIvA cell, IDH mutant, non treated, TETCD, Rep1 DIvA cell, IDH mutant, …
GSM8657519 DIvA cell, IDH mutant, non treated, TETCD, Rep2 DIvA cell, IDH mutant, …
GSM8657520 DIvA cell, IDH mutant, TETCD4-OHT over expression, Rep1 DIvA cell, IDH mutant, …
GSM8657521 DIvA cell, IDH mutant, TETCD4-OHT over expression, Rep2 DIvA cell, IDH mutant, …
GSM8657522 DIvA cell, IDH mutant, non treated, TETdCD, Rep1 DIvA cell, IDH mutant, …
GSM8657523 DIvA cell, IDH mutant, non treated, TETdCD, Rep2 DIvA cell, IDH mutant, …
GSM8657524 DIvA cell, IDH mutant, non treated, TETdCD, Rep3 DIvA cell, IDH mutant, …
GSM8657525 DIvA cell, IDH mutant, TETdCD4-OHT over expression, Rep1 DIvA cell, IDH mutant, …
GSM8657526 DIvA cell, IDH mutant, TETdCD4-OHT over expression, Rep2 DIvA cell, IDH mutant, …
GSM8657527 DIvA cell, IDH wt, non treated, input, Rep 1 DIvA cell, IDH wt, non …
GSM8657528 DIvA cell, IDH wt, non treated, input, Rep 2 DIvA cell, IDH wt, non …
GSM8657529 DIvA cell, IDH wt, non treated, input, Rep 3 DIvA cell, IDH wt, non …
GSM8657530 DIvA cell, IDH wt, non treated, input, Rep 4 DIvA cell, IDH wt, non …
GSM8657531 DIvA cell, IDH wt, 4-OHT, input, Rep 1 DIvA cell, IDH wt, 4-OH…
GSM8657532 DIvA cell, IDH wt, 4-OHT, input, Rep 2 DIvA cell, IDH wt, 4-OH…
GSM8657533 DIvA cell, IDH wt, 4-OHT, input, Rep 3 DIvA cell, IDH wt, 4-OH…
GSM8657534 DIvA cell, IDH wt, 4-OHT, input, Rep 4 DIvA cell, IDH wt, 4-OH…
GSM8657535 DIvA cell, IDH mutant, non treated, input, Rep 1 DIvA cell, IDH mutant, …
GSM8657536 DIvA cell, IDH mutant, non treated, input, Rep 2 DIvA cell, IDH mutant, …
GSM8657537 DIvA cell, IDH mutant, 4-OHT, input, Rep 1 DIvA cell, IDH mutant, …
GSM8657538 DIvA cell, IDH mutant, 4-OHT, input, Rep 2 DIvA cell, IDH mutant, …
GSM8657539 DIvA cell, IDH mutant, non treated, TETCD, input, Rep1 DIvA cell, IDH mutant, …
GSM8657540 DIvA cell, IDH mutant, non treated, TETCD, input, Rep2 DIvA cell, IDH mutant, …
GSM8657541 DIvA cell, IDH mutant, TETCD4-OHT over expression, input, Rep1 DIvA cell, IDH mutant, …

+ 77 more — browse all 117 samples with per-sample file links →

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