Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 80 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
- 80 samples: 62 distinct titles, 18 of them repeatedGroups 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.
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 GSE63339_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 PRJNA267541 and SRA study SRP049941. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 80 sample titles: 62 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.
- GSM1545960 Microglia_K4Me1_rep1
- GSM1545961 Microglia_K27Ac_rep1
- GSM1545962 Microglia_K4Me1_rep2
- GSM1545963 Microglia_K27Ac_rep2
- GSM1545964 Microglia_K4Me2_rep2
- GSM1545965 Kupffer cells_K4Me1_rep1
- GSM1545966 Kupffer cells_K27Ac_rep1
- GSM1545967 Kupffer cells_K4Me1_rep2
- GSM1545968 Kupffer cells_K27Ac_rep2
- GSM1545969 LI_K4Me1_rep1
- GSM1545970 LI_K27Ac_rep1
- GSM1545971 LI_K4Me1_rep2
- GSM1545972 LI_K27Ac_rep2
- GSM1545973 LI_K4Me2_rep2
- GSM1545974 SI_K4Me1_rep1
- GSM1545975 SI_K27Ac_rep1
- GSM1545976 SI_K4Me1_rep2
- GSM1545977 SI_K27Ac_rep2
- GSM1545978 SI_K4Me2_rep2
- GSM1545979 Lung_K4Me1_rep1
- GSM1545980 Lung_K27Ac_rep1
- GSM1545981 Lung_K4Me1_rep2
- GSM1545982 Lung_K27Ac_rep2
- GSM1545983 Lung_K4Me2_rep2
- GSM1545984 peritoneal mac_K4Me1_rep1
- GSM1545985 peritoneal mac_K27Ac_rep1
- GSM1545986 peritoneal mac_K4Me2_rep1
- GSM1545987 peritoneal mac_K4Me1_rep2
- GSM1545988 peritoneal mac_K27Ac_rep2
- GSM1545989 peritoneal mac_K4Me2_rep2
- GSM1545990 monocyte_K4Me1_rep1
- GSM1545991 monocyte_K27Ac_rep1
- GSM1545992 monocyte_K4Me1_rep2
- GSM1545993 monocyte_K27Ac_rep2
- GSM1545994 monocyte_K4Me2_rep2
- GSM1545995 Neutrophils_K4Me1_rep1
- GSM1545996 Neutrophils_K27Ac_rep1
- GSM1545997 Neutrophils_K4Me1_rep2
- GSM1545998 Neutrophils_K27Ac_rep2
- GSM1545999 Neutrophils_K4Me2_rep2
+ 40 more — browse all 80 samples with per-sample file links →
- GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 samples shares macrophage, chip-seq
- GSE325776 Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes 36 samples shares landscapes, enhancer
- GSE245648 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [RNA-seq_BMDM] 24 samples shares macrophage, enhancer
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares tissue-resident, macrophage
- GSE267584 Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 22 samples shares microenvironment, enhancer
- GSE341988 Sequential pathogen exposure normalizes the brain neuroimmune microenvironment and reveals a tissue-resident memory CD8 T cell-microglia axis shaping adult neurogenesis 8 samples shares microenvironment, tissue-resident
- GSE250376 Epigenomic and Functional Convergence Between Glucocorticoid- and IL4-Driven Macrophage Programming 13 samples shares macrophage
- GSE283906 RXR-Mediated Remodeling of Transcriptional and Chromatin Landscapes in APP Mouse Brain: Insights from Integrated Single-Cell RNA and ATAC Profiling 10 samples shares landscapes
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.