GEO series

Autophagy maintains metabolism and functional activity of a subset of aged hematopoietic stem cells [RRBS]

GSE81720 Mus musculus (mouse) DNA methylation 8 samples Submitted 2017/03/03 Platform GPL17021

At a glance

DNA methylation · mouse · 8 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 8 samples: 4 × cKO vs 4 × CntGroups 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)

Autophagy is critical for protecting HSCs from metabolic stress. Here, we used a genetic approach to inactivate autophagy in adult HSCs by deleting the Atg12 gene. We show that loss of autophagy causes accumulation of mitochondria and an oxidative phosphorylation (OXPHOS)-activated metabolic state, which drives accelerated myeloid differentiation likely through epigenetic deregulations rather than transcriptional changes, and impairs HSC self-renewal activity and regenerative potential.

Read the full summary ↓

To determine how loss of autophagy affects DNA methylation, we conducted enhanced reduce representation bisulfite sequencing (ERRBS) of purified control and Atg12 conditional knockout HSCs.

This dataset

Open GSE81720 in finder → Find more mouse methylation 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 GSE81720_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA322387 and SRA study SRP075503. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28241143) ↗

Study design

4 × cKO vs 4 × Cnt

Supports a between-group comparison across 8 samples.

How we read this: 2 replicated groups read from 8 sample titles; they account for 8 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

GSM2174434 cKO25 cKO
GSM2174435 cKO28 cKO
GSM2174436 cKO45 cKO
GSM2174437 cKO46 cKO
GSM2174438 Cnt1 Cnt
GSM2174439 Cnt34 Cnt
GSM2174440 Cnt36 Cnt
GSM2174441 Cnt37 Cnt

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GSE262396 Mitochondria-enriched hematopoietic stem cells exhibit elevated self-renewal capabilities, thriving within the context of aged bone marrow [bulk RNA-seq] 24 samples shares hematopoietic, aged, stem
GSE327449 Heterogeneity in hematopoietic stem cell enables adaptation to the aged microenvironment [scRNA-seq] 12 samples shares hematopoietic, aged, stem
GSE233879 Increased molecular and functional heterogeneity of hematopoietic stem cells contributes to age-related decline of tissue and body function 80 samples shares hematopoietic, stem
GSE272913 Dnmt3a Controls Hematopoietic Stem Cells via DNA Methylation-Independent Regulation of Telomeres 66 samples shares hematopoietic, stem
GSE286968 Deep learning identifies Pbx1 as a network hub of hematopoietic stem cell aging 60 samples shares hematopoietic, stem

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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.