Effect of SWI/SNF pertubations on H3K27ac levels during macrophage inflammatory activation [ChIP-seq_Histone]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 17 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
- 17 samples: 17 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 GSE242800_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 PRJNA1014765 and SRA study SRP459485. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 7 samples read as cases, 7 as controls.
How we read this: Read from 17 sample titles: 17 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.
- GSM7770690 WT cells, 0hr LipidA, H3K27ac ChIP [Exp1_0hr_Ctrl_H3K27ac]
- GSM7770691 WT cells, 4hr LipidA, H3K27ac ChIP [Exp1_4hr_Ctrl_H3K27ac]
- GSM7770692 ACBI1 treated cells, 4hr LipidA, H3K27ac ChIP [Exp1_4hr_ACBI1_H3K27ac]
- GSM7770693 BRM014 treated cells, 4hr LipidA, H3K27ac ChIP [Exp1_4hr_BRM014_H3K27ac]
- GSM7770694 BRDK98 treated cells, 4hr LipidA, H3K27ac ChIP [Exp1_4hr_BRDK98_H3K27ac]
- GSM7770695 Arid1A-/- cells, 4hr LipidA, H3K27ac ChIP [Exp1_4hr_ARID1AKO_H3K27ac]
- GSM7770696 WT cells, 0hr LipidA, input [Exp1_0hr_Ctrl_input]
- GSM7770697 WT cells, 4hr LipidA, input [Exp1_4hr_Ctrl_input]
- GSM7770698 ACBI1 treated cells, 4hr LipidA, input [Exp1_4hr_ACBI1_input]
- GSM7770699 BRM014 treated cells, 4hr LipidA, input [Exp1_4hr_BRM014_input]
- GSM7770700 BRDK98 treated cells, 4hr LipidA, input [Exp1_4hr_BRDK98_input]
- GSM7770701 Arid1A-/- cells, 4hr LipidA, input [Exp1_4hr_ARID1AKO_input]
- GSM7770702 WT cells, 0hr LipidA, H3K27ac ChIP [Exp2_0hr_Ctrl]
- GSM7770703 WT cells, 4hr LipidA, H3K27ac ChIP [Exp2_4hr_Ctrl]
- GSM7770704 dBrd9 treated cells, 4hr LipidA, H3K27ac ChIP [Exp2_4hr_dBrd9]
- GSM7770705 Pbrm1-/- cells, 4hr LipidA, H3K27ac ChIP [Exp2_4hr_PBRM1KO]
- GSM7770706 WT cells, 0hr LipidA, input [Exp2_input]
- GSE242799 Effect of SWI/SNF pertubations on chromatin accessibility during macrophage inflammatory activation [ATAC-seq] 40 samples shares swi, snf, pertubations, macrophage, activation
- GSE242803 SWI/SNF directed epigenetic and transcriptional response during macrophage inflammatory activation. 134 samples shares swi, snf, macrophage, activation
- GSE272549 EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ChIP-Seq] 40 samples shares swi, snf, chip-seq
- GSE249211 SWI/SNF-dependent genes are defined by their chromatin landscape [ChIP-seq_2] 24 samples shares swi, snf, chip-seq
- GSE299956 MeCP2 gene dosage-dependent neurodevelopmentally restricted defects arise by SWI/SNF-mediated aberrant activation of cell fate-determining bivalent genes [Cut & Tag] 16 samples shares swi, snf, activation
- GSE266077 Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K27ac and H3K9me3 in liver tissues from MCD and regular chow diet mice 18 samples shares h3k27ac, chip-seq, histone
- GSE272545 EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling [ATAC-Seq] 30 samples shares swi, snf
- GSE274357 Precise modulation of mSWI/SNF identified dosage-sensitive chromatin regulation [ATAC-Seq] 14 samples shares swi, snf
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.