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Unbiased profiling of clinical kinase inhibitors’ effects in activated macrophages using chromatin modifications as high-content readouts

GSE219240 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 789 samples Submitted 2024/04/16 Platform GPL24247Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 789 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
789 samples: 87 conditions, mostly in triplicateGroups 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
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitorsMolecular systems biology · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors
Gualdrini F, Rizzieri S, Polletti S et al. · Molecular systems biology 2024 · PMID 38724853 · doi:10.1038/s44320-024-00040-x
This dataset
Open GSE219240 in finder → Find more mouse RNA-seq 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 GSE219240_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 PRJNA907787 and SRA study SRP410397. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38724853) ↗
Study design
87 conditions, mostly in triplicate
IL4_1h ×3 IL4_2h ×3 IL4_30 ×3 IL4_4h ×3 LPS_1h ×3 LPS_2h ×3 LPS_30 ×3 LPS_4h ×3 +236 more

Supports a between-group comparison across 243 samples.

How we read this: 87 replicated groups read from the first 400 of 789 sample titles; they account for 243 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

+ 749 more — browse all 789 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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