GEO series
The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ChIP-seq]
GSE245647
Mus musculus (mouse)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
62 samples
Submitted 2026/07/13
Platform GPL17021
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 62 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
- 62 samples: 62 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.
Summary (written by the submitters)
Transcriptional master regulators of the myeloid lineage (like PU.1, Cebpa/b, etc.) are believed to be the main drivers of chromatin reprogramming during differentiation and polarization. Such developmental transcription factors act via their pioneer ability to open chromatin de novo and bookmark genomic regulatory sites (enhancers and promoters) to later recruit signal-dependent TFs, co-factors, and the basal transcriptional machinery.
Read the full summary ↓
However, recent studies by us and others challenged this “developmental TF-centric” mode as they suggested that signal-dependent TFs, particularly repressors, can also have a pioneer and thus safeguarding role in the MF epigenome at baseline and during acute inflammation. Such an expanded model predicts that active transcriptional repression and chromatin bookmarking by signal-dependent master regulators are key mechanisms for safeguarding the enhancer repertoire and proper priming, deployment, and resolution of an inflammatory response. Here, we show that BACH1, a heme-sensitive transcriptional repressor, acts as such a pervasive epigenomic safeguard to regulate tissue macrophage identity. We show that BACH1 is part of the core hardwired transcriptional program of ground-state macrophages shaping the chromatin accessibility of thousands of distal regulatory elements. Furthermore, BACH1 cistrome is extensive, not static but dynamic, and expanding upon different inflammatory stimuli and correlates with pre-formed and de novo formed enhancer-promoter networks. We further show that myeloid BACH1 is indispensable in vivo for tissue regeneration upon injury as it regulates the kinetics of Ly6C+ to Ly6C- transition of inflammatory macrophages and regulates the onset, the kinetics and magnitude of expression of critical inflammatory and repair-related genes. Finally, BACH1 was found to be required in vivo for competitive fitness and tissue adaptation of several tissue-resident macrophage populations (eg. lung, peritoneal macrophages), further supporting its pervasive role in acquiring and maintaining the functional specificity and diversity of tissue macrophages. Taken together, our data suggest that BACH1 acts as a signal-dependent master regulator that directly controls key transcriptional circuits during tissue macrophage subtype function, specification and inflammatory responses in vivo.
This dataset
Download · which file do I need?
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.
1 · Just have a look
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.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE245647_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
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 PRJNA1029500 and SRA study SRP466986. Searching any of these in the dataset finder brings you back here.
Study design
62 samples, each with a distinct title — no replicated groups
Supports a case/control comparison: 20 samples read as cases, 6 as controls.
How we read this: Read from 62 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.
Samples in this study
- GSM7846375 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep1)
- GSM7846376 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep2)
- GSM7846377 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep7)
- GSM7846378 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep8)
- GSM7846379 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep1)
- GSM7846380 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep2)
- GSM7846381 HDAC1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep1)
- GSM7846382 HDAC1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep2)
- GSM7846383 HDAC1 ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages (rep1)
- GSM7846384 HDAC1 ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages (rep2)
- GSM7846385 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep5, control of LPS-treated sample)
- GSM7846386 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep6, control of LPS-treated sample)
- GSM7846387 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 ng/ml LPS (rep1)
- GSM7846388 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 ng/ml LPS (rep2)
- GSM7846389 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep3, control of IL4-treated sample)
- GSM7846390 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages (rep4, control of IL4-treated sample)
- GSM7846391 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IL-4 (rep1)
- GSM7846392 BACH1 ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IL-4 (rep2)
- GSM7846393 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 ng/ml LPS (rep1)
- GSM7846394 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 ng/ml LPS (rep2)
- GSM7846395 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep1)
- GSM7846396 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep2)
- GSM7846397 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 10 ng/ml IFNb (rep1)
- GSM7846398 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 10 ng/ml IFNb (rep2)
- GSM7846399 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 10 ug/ml HMW:PIC (rep1)
- GSM7846400 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 10 ug/ml HMW:PIC (rep2)
- GSM7846401 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 1 ug/ml R848 (rep1)
- GSM7846402 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 1 ug/ml R848 (rep2)
- GSM7846403 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 1 uM ODN1286 (rep1)
- GSM7846404 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 1 uM ODN1286 (rep2)
- GSM7846405 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IFNg (rep1)
- GSM7846406 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IFNg (rep2)
- GSM7846407 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IL-4 (rep1)
- GSM7846408 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 ng/ml IL-4 (rep2)
- GSM7846409 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 uM heme and 100 ng/ml LPS (rep1)
- GSM7846410 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 uM heme and 100 ng/ml LPS (rep2)
- GSM7846411 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 uM heme (rep1)
- GSM7846412 PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 uM heme (rep2)
- GSM7846413 PolII ChIP-seq in wild type mouse bone marrow derived macrophages, untreated (rep1)
- GSM7846414 PolII ChIP-seq in wild type mouse bone marrow derived macrophages, untreated (rep2)
+ 22 more — browse all 62 samples with per-sample file links →
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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.