GEO series

Enhancing CD8 T Cell Memory by Modulating Fatty Acid Metabolism

GSE15750 Mus musculus (mouse) Expression microarray 16 samples Submitted 2009/06/05 Platform GPL1261

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: 5 × WTmouseTcell_d10 vs 5 × TRAF6KOmouseTcell_d10 vs 3 × WTmouseTcell_d6 vs 3 × TRAF6KOmouseTcell_d6Groups 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)

CD8 T cells play a crucial role in immunity to infection and cancer. They are maintained in constant numbers, but upon stimulation with antigen undergo a developmental program characterized by distinct phases encompassing the expansion and then contraction of antigen-specific populations, followed by the persistence of long-lived memory cells.

Read the full summary ↓

Although this predictable pattern of a CD8 T cell response is well established, the underlying cellular mechanisms regulating the transition to memory remain undefined. Here we show that TRAF6, an adapter protein in the TNF-receptor (TNFR) and IL-1R/TLR superfamily, regulates CD8 T cell memory development following infection by modulating fatty acid metabolism. We show that mice with a T cell-specific deletion of TRAF6 mount robust primary CD8 T cell effector responses, but have a profound defect in their ability to generate memory. This defect is CD8 T cell intrinsic and is characterized by the disappearance of antigen-specific cells in the weeks following primary immunization. Microarray analyses revealed that TRAF6-deficient CD8 T cells from early timepoints following immunization exhibit altered expression of genes that regulate fatty acid metabolism. Consistent with this, activated CD8 T cells lacking TRAF6 are unable to upregulate mitochondrial β-oxidation in response to growth factor withdrawal in vitro. Treatment with drugs that induce fatty acid oxidation enabled CD8 T cell memory generation in the absence of TRAF6. Remarkably, these treatments also increased CD8 T cell memory in wild type mice, and consequently were able to significantly improve the efficacy of an experimental anti-cancer vaccine.

This dataset

Open GSE15750 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 (GSE15750_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 PRJNA116893. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 19494812) ↗

Study design

5 × WTmouseTcell_d10 vs 5 × TRAF6KOmouseTcell_d10 vs 3 × WTmouseTcell_d6 vs 3 × TRAF6KOmouseTcell_d6

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

GSM395388 WTmouseTcell_d6_rep1 WTmouseTcell_d6
GSM395389 WTmouseTcell_d6_rep2 WTmouseTcell_d6
GSM395390 WTmouseTcell_d6_rep3 WTmouseTcell_d6
GSM395391 TRAF6KOmouseTcell_d6_rep1 TRAF6KOmouseTcell_d6
GSM395392 TRAF6KOmouseTcell_d6_rep2 TRAF6KOmouseTcell_d6
GSM395393 TRAF6KOmouseTcell_d6_rep3 TRAF6KOmouseTcell_d6
GSM395394 WTmouseTcell_d10_rep1 WTmouseTcell_d10
GSM395395 WTmouseTcell_d10_rep2 WTmouseTcell_d10
GSM395396 WTmouseTcell_d10_rep3 WTmouseTcell_d10
GSM395397 WTmouseTcell_d10_rep4 WTmouseTcell_d10
GSM395398 WTmouseTcell_d10_rep5 WTmouseTcell_d10
GSM395399 TRAF6KOmouseTcell_d10_rep1 TRAF6KOmouseTcell_d10
GSM395400 TRAF6KOmouseTcell_d10_rep2 TRAF6KOmouseTcell_d10
GSM395401 TRAF6KOmouseTcell_d10_rep3 TRAF6KOmouseTcell_d10
GSM395402 TRAF6KOmouseTcell_d10_rep4 TRAF6KOmouseTcell_d10
GSM395403 TRAF6KOmouseTcell_d10_rep5 TRAF6KOmouseTcell_d10

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GSE342096 Distinct activation programs in naïve and memory CD8 T cells govern progeny stemness and effector persistence 37 samples shares cd8, memory
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GSE306744 Pre-division TCF1 downregulation determines long-term effector and memory CD8 T cell fates [RNA-Seq] 31 samples shares cd8, memory
GSE271884 GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence [ATAC-seq]. 30 samples shares cd8, memory
GSE337898 ATAC-seq profiling of lineage-traced exhausted and memory-like CD8+ T cell subsets during tumor progression 24 samples shares cd8, memory
GSE317032 Non-cytolytic viral vaccine vectors induce durable effector-memory CD8 T cell immunity by triggering type I interferon 18 samples shares cd8, memory
GSE215759 Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells [RNA-seq] 15 samples shares cd8, memory
GSE286266 Age influences CMV-specific NK and CD8 T cell memory fates (NK cells) 12 samples shares cd8, memory

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