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mTORC1 controls the systemically-induced adaptive regulation of stem cell quiescence into GAlert

GSE55490 Mus musculus (mouse) Expression microarray 21 samples Submitted 2014/04/10 Platform GPL6246
At a glance

Expression microarray · mouse · 21 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Mus musculus (mouse)
Samples
21 samples: 9 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed expression table (series matrix) and the array files, from NCBI.
Summary (written by the submitters)
A unique property of many adult stem cells is their ability to exist in a non-cycling, quiescent state. Although quiescence serves an essential role in preserving stem cell function until the stem cell is needed in tissue homeostasis or repair, defects in quiescence can lead to an impairment in tissue function, the extent to which stem cells can regulate quiescence is unknown.
Read the full summary ↓
Here, we show that the stem cell quiescent state is composed of two distinct functional phases: G0 and an “alert” phase we term GAlert, and that stem cells actively and reversibly transition between these phases in response to injury-induced, systemic signals. Using genetic models specific to muscle stem cells (or satellite cells (SCs)), we show that mTORC1 activity is necessary and sufficient for the transition of SCs from G0 into GAlert and that signaling through the HGF receptor, cMet is also necessary. We also identify G0-to-GAlert transitions in several populations of quiescent stem cells. Quiescent stem cells that transition into GAlert possess enhanced tissue regenerative function. We propose that the transition of quiescent stem cells into GAlert functions as an 'alerting' mechanism, a novel adaptive response that positions stem cells to respond rapidly under conditions of injury and stress without requiring cell cycle entry or a cell fate commitment. We performed microarray analysis on muscle stem cells, harvested immediately after isolation, to investigate the transcriptional response these cells have to injury and the role of mTORC1 and cMet have in this response
This dataset
Open GSE55490 in finder → Find more mouse microarray datasets →
Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗
3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE55490_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA239765. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 24870234) ↗
Study design
9 conditions, mostly in duplicate
WTGFP QSC Biological Rep.1 Technical ×2 WTGFP QSC Biological Rep.2 Technical ×2 WTGFP CSC Biological Rep.1 Technical ×2 WTGFP CSC 28DPI Technical ×2 TSC1KO QSC Technical ×2 RptorKO QSC Technical ×2 RptorKO CSC Technical ×2 cMetKO QSC Technical ×2 +4 more

Supports a between-group comparison across 18 samples.

How we read this: 9 replicated groups read from 21 sample titles; they account for 18 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
Datasets on a similar topic

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