Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 170 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
- Mus musculus (mouse)
- Samples
- 170 samples: 167 distinct titles, 3 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
- 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 GSE226003_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 PRJNA939186 and SRA study SRP487243. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 23 samples read as cases, 78 as controls.
How we read this: Read from 170 sample titles: 167 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.
- GSM7061458 K562 cells, SF3B1 wild type, 4 days, replicate 1 [LRSseq]
- GSM7061459 K562 cells, SF3B1 wild type, 4 days, replicate 2 [LRSseq]
- GSM7061460 K562 cells, SF3B1 K700E, 4 days, replicate 1 [LRSseq]
- GSM7061461 K562 cells, SF3B1 K700E, 4 days, replicate 2 [LRSseq]
- 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
- GSM7061478 K562 cells, SF3B1 wild type, 4 days, replicate 1, IP [CDK9ChIPseq_K562_WT_IP_Replicate1]
- GSM7061479 K562 cells, SF3B1 wild type, 4 days, replicate 2, IP [CDK9ChIPseq_K562_WT_IP_Replicate2]
- GSM7061480 K562 cells, SF3B1 K700E, 4 days, replicate 1, IP [CDK9ChIPseq_K562_SF3B1K700E_IP_Replicate1]
- GSM7061481 K562 cells, SF3B1 K700E, 4 days, replicate 2, IP [CDK9ChIPseq_K562_SF3B1K700E_IP_Replicate2]
- GSM7061482 K562 cells, SF3B1 wild type, 4 days, replicate 1, Input [CDK9ChIPseq_K562_WT_Input_Replicate1]
- GSM7061483 K562 cells, SF3B1 wild type, 4 days, replicate 2, Input [CDK9ChIPseq_K562_WT_Input_Replicate2]
- GSM7061484 K562 cells, SF3B1 K700E, 4 days, replicate 1, Input [CDK9ChIPseq_K562_SF3B1K700E_Input_Replicate1]
- GSM7061485 K562 cells, SF3B1 K700E, 4 days, replicate 2, Input [CDK9ChIPseq_K562_SF3B1K700E_Input_Replicate2]
- GSM7061486 K562 cells, SF3B1 wild type, 4 days, replicate 1 [RNAPIINTDChIPseq_K562_WT_Replicate1]
- GSM7061487 K562 cells, SF3B1 wild type, 4 days, replicate 2 [RNAPIINTDChIPseq_K562_WT_Replicate2]
- GSM7061488 K562 cells, SF3B1 K700E, 4 days, replicate 1 [RNAPIINTDChIPseq_K562_SF3B1K700E_Replicate1]
- GSM7061489 K562 cells, SF3B1 K700E, 4 days, replicate 2 [RNAPIINTDChIPseq_K562_SF3B1K700E_Replicate2]
- GSM7061490 K562 cells, SF3B1 wild type, 4 days, replicate 1 [TTTLseq_K562_WT_Replicate1]
- GSM7061491 K562 cells, SF3B1 wild type, 4 days, replicate 2 [TTTLseq_K562_WT_Replicate2]
- GSM7061492 K562 cells, SF3B1 K700E, 4 days, replicate 1 [TTTLseq_K562_SF3B1K700E_Replicate1]
- GSM7061493 K562 cells, SF3B1 K700E, 4 days, replicate 2 [TTTLseq_K562_SF3B1K700E_Replicate2]
- GSM7061494 K562 cells, U2AF1 wild type, 4 days, replicate 1 [TTTLseq_K562_U2WT_Replicate1]
- GSM7061495 K562 cells, U2AF1 wild type, 4 days, replicate 2 [TTTLseq_K562_U2WT_Replicate2]
- GSM7061496 K562 cells,U2AF1 S34F, 4 days, replicate 1 [TTTLseq_K562_U2S34F_Replicate1]
- GSM7061497 K562 cells, U2AF1 S34F, 4 days, replicate 2 [TTTLseq_K562_U2S34F_Replicate2]
+ 130 more — browse all 170 samples with per-sample file links →
- GSE202126 Single-cell Total-RNA Profiling Unveils Regulatory Hubs of Transcription Factors 1089 samples shares transcription
- GSE267145 The transcription factor ZNF469 regulates collagen production in liver fibrosis 508 samples shares transcription
- GSE102556 Sex-specific Transcriptional Signatures in Human Depression 341 samples shares transcription
- GSE260456 DOT1L provides transcriptional memory through PRC1.1 antagonism [RNA-seq] 180 samples shares transcription
- GSE188417 The PAF1 Complex Regulates Transcriptional Termination and Reinitiation 122 samples shares transcription
- GSE20281 The transcriptional network for mesenchymal transformation of brain tumours 108 samples shares transcription
- GSE63782 Transcriptional plasticity promotes primary and acquired resistance to BET bromodomain inhibition 103 samples shares transcription
- GSE271891 The PNUTS phosphatase complex controls transcription pause release [ChIP-Seq] 94 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.