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Autophagy engaging and non-engaging hematopoietic stem cells

GSE229137 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 607 samples Submitted 2024/05/15 Platform GPL21103Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 607 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
607 samples: 10 conditions, mostly in duplicateGroups 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
Autophagy counters inflammation-driven glycolytic impairment in aging hematopoietic stem cellsCell stem cell · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Autophagy counters inflammation-driven glycolytic impairment in aging hematopoietic stem cells
Dellorusso PV, Proven MA, Calero-Nieto FJ et al. · Cell stem cell 2024 · PMID 38754428 · doi:10.1016/j.stem.2024.04.020
This dataset
Open GSE229137 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 GSE229137_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 PRJNA958188 and SRA study SRP504083. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38754428) ↗
Study design
10 conditions, mostly in duplicate
GFP-LC3 oHSC_LO ×90 GFP-LC3 oHSC_MID ×90 GFP-LC3 oHSC_HI ×89 GFP-LC3 yHSC ×87 Young ×5 AThi oHSC ×3 ATlo oHSC ×3 yHSC ×2 +29 more

Supports a between-group comparison across 373 samples.

How we read this: 10 replicated groups read from the first 400 of 607 sample titles; they account for 373 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

+ 567 more — browse all 607 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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