GEO series

Regulatory T cells from injured skeletal muscle

GSE50096 Mus musculus (mouse) Expression microarray 24 samples Submitted 2013/12/15 Platform GPL6246

At a glance

Expression microarray · mouse · 24 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Mus musculus (mouse)
Samples: 24 samples: 8 conditions, mostly in triplicateGroups 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 phenotypically and functionally distinct population of CD4+ Foxp3+ T cells (Tregs) rapidly accumulates in acutely injured skeletal muscle of mice, just as invading myeloid-lineage cells switch from a pro-inflammatory to a pro-regenerative state. Analysis of gene expression of Tregs and CD4+Foxp3- T cells (Tconvs) from injured muscle and spleen revealed that the transcriptome of muscle Treg cells is distinct from that of splenic Tregs.

Read the full summary ↓

A set of genes is uniquely expressed by muscle Tregs, while another set is over-expressed by the two muscle populations vis-à-vis their two spleen counterparts.

This dataset

Open GSE50096 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 (GSE50096_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 PRJNA216021. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 24315098) ↗

Study design

8 conditions, mostly in triplicate

TC.2wkINJ.Mu# ×3 TC.2wkINJ.Sp# ×3 TC.4dINJ.Mu# ×3 TC.4dINJ.Sp# ×3 TR.2wkINJ.Mu# ×3 TR.2wkINJ.Sp# ×3 TR.4dINJ.Mu# ×3 TR.4dINJ.Sp# ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM1214169 TC.2wkINJ.Mu#1 TC.2wkINJ.Mu#
GSM1214170 TC.2wkINJ.Mu#2 TC.2wkINJ.Mu#
GSM1214171 TC.2wkINJ.Mu#3 TC.2wkINJ.Mu#
GSM1214172 TC.2wkINJ.Sp#1 TC.2wkINJ.Sp#
GSM1214173 TC.2wkINJ.Sp#2 TC.2wkINJ.Sp#
GSM1214174 TC.2wkINJ.Sp#3 TC.2wkINJ.Sp#
GSM1214175 TC.4dINJ.Mu#1 TC.4dINJ.Mu#
GSM1214176 TC.4dINJ.Mu#2 TC.4dINJ.Mu#
GSM1214177 TC.4dINJ.Mu#3 TC.4dINJ.Mu#
GSM1214178 TC.4dINJ.Sp#1 TC.4dINJ.Sp#
GSM1214179 TC.4dINJ.Sp#2 TC.4dINJ.Sp#
GSM1214180 TC.4dINJ.Sp#3 TC.4dINJ.Sp#
GSM1214181 TR.2wkINJ.Mu#1 TR.2wkINJ.Mu#
GSM1214182 TR.2wkINJ.Mu#2 TR.2wkINJ.Mu#
GSM1214183 TR.2wkINJ.Mu#3 TR.2wkINJ.Mu#
GSM1214184 TR.2wkINJ.Sp#1 TR.2wkINJ.Sp#
GSM1214185 TR.2wkINJ.Sp#2 TR.2wkINJ.Sp#
GSM1214186 TR.2wkINJ.Sp#3 TR.2wkINJ.Sp#
GSM1214187 TR.4dINJ.Mu#1 TR.4dINJ.Mu#
GSM1214188 TR.4dINJ.Mu#2 TR.4dINJ.Mu#
GSM1214189 TR.4dINJ.Mu#3 TR.4dINJ.Mu#
GSM1214190 TR.4dINJ.Sp#1 TR.4dINJ.Sp#
GSM1214191 TR.4dINJ.Sp#2 TR.4dINJ.Sp#
GSM1214192 TR.4dINJ.Sp#3 TR.4dINJ.Sp#

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