Effect of SWI/SNF pertubations on chromatin accessibility during macrophage inflammatory activation [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 40 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
- 40 samples: 40 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.
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 GSE242799_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 PRJNA1014766 and SRA study SRP459486. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 18 samples read as cases, 19 as controls.
How we read this: Read from 40 sample titles: 40 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.
- GSM7770664 WT cells, 0hr LipidA [Exp1_0hr_Ctrl_rep1 ATAC-seq]
- GSM7770665 WT cells, 0hr LipidA [Exp1_0hr_Ctrl_rep2 ATAC-seq]
- GSM7770666 WT cells, 4hr LipidA [Exp1_4hr_Ctrl_rep1 ATAC-seq]
- GSM7770667 WT cells, 4hr LipidA [Exp1_4hr_Ctrl_rep2 ATAC-seq]
- GSM7770668 ACBI1 treated cells, 4hr LipidA [Exp1_4hr_ACBI1_rep1 ATAC-seq]
- GSM7770669 ACBI1 treated cells, 4hr LipidA [Exp1_4hr_ACBI1_rep2 ATAC-seq]
- GSM7770670 BRDK98 treated cells, 4hr LipidA [Exp1_4hr_BRDK98_rep1 ATAC-seq]
- GSM7770671 BRDK98 treated cells, 4hr LipidA [Exp1_4hr_BRDK98_rep2 ATAC-seq]
- GSM7770672 WT cells, 0hr LipidA [Exp2_0hr_Ctrl_rep1 ATAC-seq]
- GSM7770673 WT cells, 4hr LipidA [Exp2_4hr_Ctrl_rep1 ATAC-seq]
- GSM7770674 BRM014 treated cells, 4hr LipidA [Exp2_4hr_BRM014_rep1 ATAC-seq]
- GSM7770675 Arid1a-/- cells, 4hr LipidA [Exp2_4hr_ARID1AKO_rep1 ATAC-seq]
- GSM7770676 WT cells, 0hr LipidA [Exp3_0hr_Ctrl_rep1 ATAC-seq]
- GSM7770677 WT cells, 0hr LipidA [Exp3_0hr_Ctrl_rep2 ATAC-seq]
- GSM7770678 WT cells, 1hr LipidA [Exp3_1hr_Ctrl_rep1 ATAC-seq]
- GSM7770679 WT cells, 1hr LipidA [Exp3_1hr_Ctrl_rep2 ATAC-seq]
- GSM7770680 WT cells, 4hr LipidA [Exp3_4hr_Ctrl_rep1 ATAC-seq]
- GSM7770681 WT cells, 4hr LipidA [Exp3_4hr_Ctrl_rep2 ATAC-seq]
- GSM7770682 dBrd9 treated cells, 4hr LipidA [Exp3_4hr_dBrd9_rep1 ATAC-seq]
- GSM7770683 dBrd9 treated cells, 4hr LipidA [Exp3_4hr_dBrd9_rep2 ATAC-seq]
- GSM7770684 WT cells, 0hr LipidA [Exp4_0hr_rep1 ATAC-seq]
- GSM7770685 WT cells, 0hr LipidA [Exp4_0hr_rep2 ATAC-seq]
- GSM7770686 WT cells, 4hr LipidA [Exp4_4hr_rep1 ATAC-seq]
- GSM7770687 WT cells, 4hr LipidA [Exp4_4hr_rep2 ATAC-seq]
- GSM7770688 Pbrm1-/- cells, 4hr LipidA [Exp4_4hr_PBRM1KO_rep1 ATAC-seq]
- GSM7770689 Pbrm1-/- cells, 4hr LipidA [Exp4_4hr__PBRM1KO_rep2 ATAC-seq]
- GSM8066917 BRDK98 treated cells, 0hr LipidA [Exp1_0hr_BRDK98_rep1]
- GSM8066918 BRDK98 treated cells, 0hr LipidA [Exp1_0hr_BRDK98_rep2]
- GSM8066919 BRM014 treated cells, 0hr LipidA [Exp2_0hr_BRM014_rep1]
- GSM8066920 BRM014 treated cells, 4hr LipidA [Exp4_4hr_BRM014_rep1]
- GSM8066921 BRM014 treated cells, 4hr LipidA [Exp4_4hr_BRM014_rep2]
- GSM8066922 WT cells, 0hr LipidA [Exp5_0hr_Ctrl_rep1]
- GSM8066923 ACBI1 treated cells, 0hr LipidA [Exp5_0hr_ACBI1_rep1]
- GSM8066924 WT cells, 1hr LipidA [Exp5_1hr_Ctrl_rep1]
- GSM8066925 WT cells, 1hr LipidA [Exp5_1hr_Ctrl_rep2]
- GSM8066926 ACBI1 treated cells, 1hr LipidA [Exp5_1hr_ACBI1_rep1]
- GSM8066927 ACBI1 treated cells, 1hr LipidA [Exp5_1hr_ACBI1_rep2]
- GSM8066928 BRM014 treated cells, 1hr LipidA [Exp5_1hr_BRM014_rep1]
- GSM8066929 BRM014 treated cells, 1hr LipidA [Exp5_1hr_BRM014_rep2]
- GSM8066930 BRDK98 treated cells, 1hr LipidA [Exp5_1hr_BRDK98_rep1]
- GSE242800 Effect of SWI/SNF pertubations on H3K27ac levels during macrophage inflammatory activation [ChIP-seq_Histone] 17 samples shares swi, snf, pertubations, macrophage, activation
- GSE274357 Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [ATAC-Seq] 14 samples shares swi, snf, chromatin, atac-seq
- GSE242803 SWI/SNF directed epigenetic and transcriptional response during macrophage inflammatory activation. 134 samples shares swi, snf, macrophage, activation
- GSE272545 EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ATAC-Seq] 30 samples shares swi, snf, atac-seq
- GSE249211 SWI/SNF-dependent genes are defined by their chromatin landscape [ChIP-seq_2] 24 samples shares swi, snf, chromatin
- GSE226954 SWI/SNF-dependent genes are defined by their chromatin landscape 61 samples shares swi, snf, chromatin
- GSE268206 CRISPR screen decodes SWI/SNF chromatin remodeling complex assembly 56 samples shares swi, snf, chromatin
- GSE248369 The Swi/Snf chromatin remodeling complex regulates pancreatic endocrine cell expansion and differentiation in vivo 10 samples shares swi, snf, chromatin
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.