TGF-β and RAS jointly unmask primed enhancers to drive metastasis (ATAC-Seq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 6 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
- TGF-β and RAS jointly unmask primed enhancers to drive metastasisCell · 2024
Read the full summary ↓
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 GSE256013_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 PRJNA1077391 and SRA study SRP490099. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8084134 ATAC-WT_SB_Rep1 ATAC-WT_SB
- GSM8084135 ATAC-WT_SB_Rep2 ATAC-WT_SB
- GSM8084136 ATAC-WT_TGFb_Rep1 ATAC-WT_TGFb
- GSM8084137 ATAC-WT_TGFb_Rep2 ATAC-WT_TGFb
- GSM8084138 ATAC-Rreb1KO_SB_Rep1 ATAC-Rreb1KO_SB
- GSM8084139 ATAC-Rreb1KO_SB_Rep2 ATAC-Rreb1KO_SB
- GSM8084140 ATAC-Rreb1KO_TGFb_Rep1 ATAC-Rreb1KO_TGFb
- GSM8084141 ATAC-Rreb1KO_TGFb_Rep2 ATAC-Rreb1KO_TGFb
- GSM8084142 ATAC-Ino80KO_SB_Rep1 ATAC-Ino80KO_SB
- GSM8084143 ATAC-Ino80KO_SB_Rep2 ATAC-Ino80KO_SB
- GSM8084144 ATAC-Ino80KO_TGFb_Rep1 ATAC-Ino80KO_TGFb
- GSM8084145 ATAC-Ino80KO_TGFb_Rep2 ATAC-Ino80KO_TGFb
- GSE279088 Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis [ATAC-Seq] 74 samples shares ras, atac-seq
- GSE233039 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ATAC-Seq] 18 samples shares ras, atac-seq
- GSE319596 Lineage identity governs oncogene dependence in murine NSCLC models of KRAS inhibitor resistance [ATAC-Seq] 16 samples shares ras, atac-seq
- GSE329244 Polycomb erasers BAP1 and UTX are dispensable for rapid bivalent gene activation but essential for enhancer establishment [ChIP-seq] 64 samples shares ras
- GSE268146 Integrator complex bridges TFIID and RNA polymerase II to maintain pluripotency during development (ChIP-Seq) 38 samples shares ras
- GSE324933 DGCR8 promotes RNA polymerase II pause release independently of DROSHA [ChIP-seq] 32 samples shares ras
- GSE326112 Interleukin-12 drives a rapid STAT4/DDX5-dependent change in the RNA polymerase II landscape for IFN-γ production by NK cells [CUT&RUN] 18 samples shares ras
- GSE299381 KAT6A Chimeras Forms a Self-Reinforcing Epigenetic Module with NURF and MLL/COMPASS in AML [ChIP-Seq] 13 samples shares ras
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.