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Autophagy enforces functional integrity of regulatory T cells by coupling environmental cues and metabolic homeostasis

GSE75218 Mus musculus (mouse) Expression microarray 16 samples Submitted 2016/01/25 Platform GPL16570
At a glance

Expression microarray · mouse · 16 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Mus musculus (mouse)
Samples
16 samples: 4 × Atg7+/- Treg cells untreated vs 4 × Atg7-/- Treg cells untreated vs 4 × Atg7+/- Treg cells rapamycin treated vs 4 × Atg7-/- Treg cells rapamycin treatedGroups 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)
Regulatory T (Treg) cells respond to immune and inflammatory signals to mediate immunosuppression, but how the functional integrity of Treg cells is maintained under activating environments is unclear. Here we show that autophagy is active in Treg cells and supports their lineage stability and survival fitness. Treg cell–specific deletion of Atg7 or Atg5, both essential genes in autophagy, leads to loss of Treg cells, greater tumor resistance and development of inflammatory disorders.
Read the full summary ↓
Atg7-deficient Treg cells show increased apoptosis and readily lose expression of the transcription factor Foxp3, especially after activation. Mechanistically, autophagy deficiency upregulates mTORC1 and c-Myc and glycolytic metabolism, which contributes to defective Treg function. Therefore, autophagy couples environmental signals and metabolic homeostasis to protect lineage and survival integrity of Treg cells in activating contexts.
This dataset
Open GSE75218 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 (GSE75218_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 PRJNA302814. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 26808230) ↗
Study design
4 × Atg7+/- Treg cells untreated vs 4 × Atg7-/- Treg cells untreated vs 4 × Atg7+/- Treg cells rapamycin treated vs 4 × Atg7-/- Treg cells rapamycin treated

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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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