SWI/SNF-dependent genes are defined by their chromatin landscape
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 61 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
- 61 samples: 61 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
- SWI/SNF-dependent genes are defined by their chromatin landscapeCell reports · 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 GSE226954_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 PRJNA942303 and SRA study SRP426283. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 20 samples read as cases, 8 as controls.
How we read this: Read from 61 sample titles: 61 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.
- GSM7088720 DMSO treated cells, biological rep1 (ATAC-seq)
- GSM7088721 DMSO treated cells, biological rep2 (ATAC-seq)
- GSM7088722 BRM014 treated cells during 6h, biological rep1 (ATAC-seq)
- GSM7088723 BRM014 treated cells during 6h, biological rep2 (ATAC-seq)
- GSM7088724 BRM014 treated cells during 30h, biological rep1 (ATAC-seq)
- GSM7088725 BRM014 treated cells during 30h, biological rep2 (ATAC-seq)
- GSM7088726 input Chromatin (ChIP-seq)
- GSM7088727 H3K27me3 ChIP (ChIP-seq)
- GSM7088736 DMSO treated cells during 6h, biological rep1 (ChRNA-seq)
- GSM7088737 DMSO treated cells during 6h, biological rep2 (ChRNA-seq)
- GSM7088738 DMSO treated cells during 30h, biological rep1 (ChRNA-seq)
- GSM7088739 DMSO treated cells during 30h, biological rep2 (ChRNA-seq)
- GSM7088740 BRM014 treated cells during 6h, biological rep1 (ChRNA-seq)
- GSM7088741 BRM014 treated cells during 6h, biological rep2 (ChRNA-seq)
- GSM7088742 BRM014 treated cells during 30h, biological rep1 (ChRNA-seq)
- GSM7088743 BRM014 treated cells during 30h, biological rep2 (ChRNA-seq)
- GSM7088744 DMSO treated cells, biological rep1 (Cut&Tag)
- GSM7088745 DMSO treated cells, biological rep2 (Cut&Tag)
- GSM7088746 BRM014 treated cells during 30h, biological rep1 (Cut&Tag)
- GSM7088747 BRM014 treated cells during 30h, biological rep2 (Cut&Tag)
- GSM7088748 DMSO treated cells, biological rep1 (MNase-seq)
- GSM7088749 DMSO treated cells, biological rep2 (MNase-seq)
- GSM7088750 DMSO treated cells, without crosslinking (MNase-seq)
- GSM7088751 BRM014 treated cells during 6h, biological rep1 (MNase-seq)
- GSM7088752 BRM014 treated cells during 6h, biological rep2 (MNase-seq)
- GSM7088753 BRM014 treated cells during 6h, without crosslinking (MNase-seq)
- GSM7088754 BRM014 treated cells during 30h, biological rep1 (MNase-seq)
- GSM7088755 BRM014 treated cells during 30h, biological rep2 (MNase-seq)
- GSM7088756 BRM014 treated cells during 30h, without crosslinking (MNase-seq)
- GSM7088779 DMSO treated cells during 6h, biological rep1 (RNA-seq)
- GSM7088780 DMSO treated cells during 6h, biological rep2 (RNA-seq)
- GSM7088781 DMSO treated cells during 30h, biological rep1 (RNA-seq)
- GSM7088782 DMSO treated cells during 30h, biological rep2 (RNA-seq)
- GSM7088783 BRM014 treated cells during 6h, biological rep1 (RNA-seq)
- GSM7088784 BRM014 treated cells during 6h, biological rep2 (RNA-seq)
- GSM7088785 BRM014 treated cells during 30h, biological rep1 (RNA-seq)
- GSM7088786 BRM014 treated cells during 30h, biological rep2 (RNA-seq)
- GSM7928368 NmuMG, BRD9, rep1, ChIP
- GSM7928369 NmuMG, BRD9, rep2, ChIP
- GSM7928370 NmuMG, DPF2, rep1, ChIP
+ 21 more — browse all 61 samples with per-sample file links →
- GSE248369 The Swi/Snf chromatin remodeling complex regulates pancreatic endocrine cell expansion and differentiation in vivo 10 samples shares swi, chromatin
- GSE283483 Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression programs in the hippocampus 160 samples shares chromatin, defined
- GSE269191 ZEB2 is a Master Switch Controlling the Tumor-Associated Macrophage Program [in vivo] 145 samples shares swi
- GSE250551 Targeting inflammation with chimeric antigen receptor macrophages using a signal switch 32 samples shares swi
- GSE234248 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [RNA-seq] 24 samples shares swi
- GSE234251 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [Mnase-seq] 21 samples shares swi
- GSE247845 FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma [RNA-Seq] 20 samples shares swi
- GSE269187 ZEB2 is a Master Switch Controlling the Tumor-Associated Macrophage Program [in vitro] 17 samples shares swi
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.