Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [ATAC-seq]
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
- Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscapeMolecular cell · 2024
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE225993_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA939532 and SRA study SRP425041. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 6 as controls.
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.
- GSM7061462 K562 cells, SF3B1 wild type, 4 days, replicate 1, ATAC-seq
- GSM7061463 K562 cells, SF3B1 wild type, 4 days, replicate 2, ATAC-seq
- GSM7061464 K562 cells, SF3B1K700E, 4 days, replicate 1, ATAC-seq
- GSM7061465 K562 cells, SF3B1K700E, 4 days, replicate 2, ATAC-seq
- GSM7061466 CD34 cells, healthy volunteer, replicate 1, ATAC-seq
- GSM7061467 CD34 cells, healthy volunteer, replicate 2, ATAC-seq
- GSM7061468 CD34 cells, healthy volunteer, replicate 3, ATAC-seq
- GSM7061469 CD34 cells, SF3B1-mutant MDS, replicate 1, ATAC-seq
- GSM7061470 CD34 cells, SF3B1-mutant MDS, replicate 2, ATAC-seq
- GSM7061471 CD34 cells, SF3B1-mutant MDS, replicate 3, ATAC-seq
- GSM7061472 CD34 cells, SF3B1-mutant MDS, replicate 4, ATAC-seq
- GSM7061473 CD34 cells, SF3B1-mutant MDS, replicate 5, ATAC-seq
- GSM7061474 CD34 cells, SF3B1-mutant MDS, replicate 6, ATAC-seq
- GSM7061475 cKIT+Sca1+Lin- cells, Murine Sf3b1 WT, replicate 1, ATAC-seq
- GSM7061476 cKIT+Sca1+Lin- cells, Murine Sf3b1 K700E, replicate 1, ATAC-seq
- GSM7061477 cKIT+Sca1+Lin- cells, Murine Sf3b1 K700E, replicate 2, ATAC-seq
- GSE274098 Recurrent FGFR-alterations are frequent oncogenic drivers and therapeutic targets in pediatric low-grade gliomas 68 samples shares alterations, oncogenic
- GSE226204 Neurological Cockayne Syndrome Results from R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation 37 samples shares transcription, elongation
- GSE253935 Heterogeneous Cardiac- and Neural Crest-Derived Aortic Smooth Muscle Cells have Similar Transcriptional Changes after TGFβ Signaling Disruption 32 samples shares transcription, disruption
- GSE261351 Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples 278 samples shares transcription
- GSE286875 Improved spike-in normalization clarifies the relationship between active histone modifications and transcription 244 samples shares transcription
- GSE260742 DOT1L provides transcriptional memory through PRC1.1 antagonism [ChIP-Seq] 158 samples shares transcription
- GSE240599 An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs 130 samples shares transcription
- GSE292300 A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: ChIP-seq 76 samples shares transcription
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.