SWI/SNF directed epigenetic and transcriptional response during macrophage inflammatory activation.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 134 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
- 134 samples: 134 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
- Collaboration between distinct SWI/SNF chromatin remodeling complexes directs enhancer selection and activation of macrophage inflammatory genesImmunity · 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 GSE242803_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 PRJNA1014761 and SRA study SRP459485. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 47 samples read as cases, 75 as controls.
How we read this: Read from 134 sample titles: 134 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]
- 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]
+ 94 more — browse all 134 samples with per-sample file links →
- GSE99296 α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming 18 samples shares epigenetic, macrophage, activation
- GSE269191 ZEB2 is a Master Switch Controlling the Tumor-Associated Macrophage Program [in vivo] 145 samples shares swi, macrophage
- GSE250551 Targeting inflammation with chimeric antigen receptor macrophages using a signal switch 32 samples shares swi, macrophage
- GSE269187 ZEB2 is a Master Switch Controlling the Tumor-Associated Macrophage Program [in vitro] 17 samples shares swi, macrophage
- GSE281007 Lysine Crotonylation Acts as an Epigenetic Switch for Glutamate Neurotransmission and Spatial Memory 12 samples shares swi, epigenetic
- GSE292063 Pre-existing epigenetic state and differential NF-kB activation shape type 2 immune cell responses 61 samples shares epigenetic, activation
- GSE276632 Reciprocal genetic screens identify epigenetics factors controlling epidermal cell activation. 262 samples shares epigenetic, activation
- GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares macrophage, activation
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.