GEO series

Epigenomic and Functional Convergence Between Glucocorticoid- and IL4-Driven Macrophage Programming [ATAC-seq]

GSE248042 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2024/09/03 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 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: 24 samples: 6 conditions, mostly with about 4 replicates eachGroups 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: Mechanisms of epigenomic and functional convergence between glucocorticoid- and IL4-driven macrophage programmingNature communications · 2024

Summary (written by the submitters)

Macrophages adopt distinct phenotypes in response to environmental cues, with type-2 cytokine interleukin-4 (IL4) promoting a tissue-repair homeostatic state (M2IL4). Glucocorticoids - widely used anti-inflammatory therapeutics - reportedly impart a similar phenotype (M2GC), however how or to what extent these populations functionally converge is unknown.

Read the full summary ↓

We show that M2IL4 and M2GC transcriptomes share a striking overlap mirrored by a shift in chromatin landscape in both common and signal-specific gene subsets. This core homeostatic program is enacted by transcriptional effectors KLF4 and the GC receptor (GR), whose genome-wide occupancy and actions are integrated in a stimulus-specific manner by the nuclear receptor cofactor GRIP1. Indeed, 35% of the shared IL4- vs. GC-elicited transcriptomic changes were GRIP1-dependent. Consistently, GRIP1 loss attenuated M2IL4 and M2GC phagocytic activity in vitro and macrophage tissue-repair properties in the murine colitis model in vivo. These findings provide a mechanistic framework for homeostatic macrophage programming by distinct signals, to better inform GR-targeting drug design.

Published in

Mechanisms of epigenomic and functional convergence between glucocorticoid- and IL4-driven macrophage programming

Deochand DK, Dacic M, Bale MJ et al. · Nature communications 2024 · PMID 39424780 · doi:10.1038/s41467-024-52942-x

This dataset

Open GSE248042 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →

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.

Series matrix ↓

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 GSE248042_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

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.

Raw reads on ENA ↗

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 PRJNA1041449 and SRA study SRP472415. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39424780) ↗

Study design

6 conditions, mostly with about 4 replicates each

GRIP1 KO, vehicle, 24h, ×4 GRIP1 KO, Dexamethasone, 24h, ×4 GRIP1 KO, IL4, 24h, ×4 Wild type, IL4, 24h, ×4 Wild type, Dexamethasone , 24h, ×3 Wild type, vehicle, 24h, ×2 Wild type, Dexamethasone, 24h, ×1 Wild type, vehicle ,24h, ×1 +1 more

Supports a between-group comparison across 21 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 21 of them. 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

GSM7905114 GRIP1 KO, vehicle, 24h, rep1 GRIP1 KO, vehicle, 24h,
GSM7905115 GRIP1 KO, Dexamethasone, 24h, rep1 GRIP1 KO, Dexamethasone…
GSM7905116 GRIP1 KO, IL4, 24h, rep1 GRIP1 KO, IL4, 24h,
GSM7905117 GRIP1 KO, vehicle, 24h, rep2 GRIP1 KO, vehicle, 24h,
GSM7905118 GRIP1 KO, Dexamethasone, 24h, rep2 GRIP1 KO, Dexamethasone…
GSM7905119 GRIP1 KO, IL4, 24h, rep2 GRIP1 KO, IL4, 24h,
GSM7905120 GRIP1 KO, vehicle, 24h, rep3 GRIP1 KO, vehicle, 24h,
GSM7905121 GRIP1 KO, Dexamethasone, 24h, rep3 GRIP1 KO, Dexamethasone…
GSM7905122 GRIP1 KO, IL4, 24h, rep3 GRIP1 KO, IL4, 24h,
GSM7905123 GRIP1 KO, vehicle, 24h, rep4 GRIP1 KO, vehicle, 24h,
GSM7905124 GRIP1 KO, Dexamethasone, 24h, rep4 GRIP1 KO, Dexamethasone…
GSM7905125 GRIP1 KO, IL4, 24h, rep4 GRIP1 KO, IL4, 24h,
GSM7905126 Wild type, vehicle, 24h, rep1 Wild type, vehicle, 24h,
GSM7905127 Wild type, Dexamethasone, 24h, rep1
GSM7905128 Wild type, IL4, 24h, rep1 Wild type, IL4, 24h,
GSM7905129 Wild type, vehicle, 24h, rep2 Wild type, vehicle, 24h,
GSM7905130 Wild type, Dexamethasone , 24h, rep2 Wild type, Dexamethason…
GSM7905131 Wild type, IL4, 24h, rep2 Wild type, IL4, 24h,
GSM7905132 Wild type, vehicle ,24h, rep3
GSM7905133 Wild type, Dexamethasone , 24h, rep3 Wild type, Dexamethason…
GSM7905134 Wild type, IL4, 24h, rep3 Wild type, IL4, 24h,
GSM7905135 Wild type, vehicle , 24h, rep4
GSM7905136 Wild type, Dexamethasone , 24h, rep4 Wild type, Dexamethason…
GSM7905137 Wild type, IL4, 24h, rep4 Wild type, IL4, 24h,

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