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Series GSE12465 Query DataSets for GSE12465
Status Public on May 20, 2009
Title Transcriptional signatures of Itk-deficiency using CD3+, CD4+ and CD8+ T-cells
Organism Mus musculus
Experiment type Expression profiling by array
Summary The Tec-family kinase Itk plays an important role during T-cell activation and function, and controls also conventional versus innate-like T-cell development. We have characterized the transcriptome of Itk-deficient CD3+ T-cells, including CD4+ and CD8+ subsets, using Affymetrix microarrays. The largest difference between Itk-/- and Wt CD3+ T-cells was found in unstimulated cells, e.g. for killer cell lectin-like receptors. Compared to anti-CD3-stimulation, anti-CD3/CD28 significantly decreased the number of transcripts suggesting that the CD28 co-stimulatory pathway is mainly independent of Itk. The signatures of CD4+ and CD8+ T-cell subsets identified a greater differential expression than in total CD3+ cells. Cyclosporin (CsA)-treatment had a stronger effect on transcriptional regulation than Itk-deficiency, suggesting that only a fraction of TCR-mediated calcineurin/NFAT-activation is dependent on Itk. Bioinformatic analysis of NFAT-sites of the group of transcripts similarly regulated by Itk-deficiency and CsA-treatment, followed by chromatin-immunoprecipitation, revealed NFATc1-binding to the Bub1, IL7R, Ctla2a, Ctla2b, and Schlafen1 genes. Finally, to identify transcripts that are regulated by Tec-family kinases in general, we compared the expression profile of Itk-deficient T-cells with that of Btk-deficient B-cells and a common set of transcripts was found. Taken together, our study provides a general overview about the global transcriptional changes in the absence of Itk.
 
Overall design CD3+ CD4+ and CD8+ T-cells from pooled suspensions of spleen and lymph nodes of Wt and Itk knockout mice on C57BL/6 background were isolated after negative depletion. Unstimulated as well as stimulated T-cells were studied. Stimulations were done with anti-CD3 (1 mg/ml) for 24 hrs. For the CD4+ T-cells we collected triplicates from the Itk knockout mice and duplicates from the Wt group. For the CD8+ T-cells, we got duplicates from Itk knockout , while we obtained a single sample from Wt owing to the low cell yield for resting Wt CD8+ T-cells. After CD3-stimulation we got a single sample from the CD8+ subset of both Wt and Itk knockout, while for the CD4+ subsets we collected duplicates.
 
Contributor(s) Blomberg KE, Boucheron N, Lindvall JM, Yu L, Raberger J, Berglöf A, Ellmeier W, Smith CI
Citation(s) 19450280
Submission date Aug 15, 2008
Last update date Feb 11, 2019
Contact name Emelie Blomberg
E-mail(s) emelie.blomberg@ki.se
Organization name Karolinska Institutet
Department Department of Laboratory Medicine, Clinical Research Center
Lab MCG
Street address Novum level 5
City Huddinge
ZIP/Postal code SE-141 86
Country Sweden
 
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (14)
GSM313189 Wild type CD4+ unstimulated 1
GSM313190 Wild type CD4+ unstimulated 2
GSM313191 Itk knockout CD4+ unstimulated 1
This SubSeries is part of SuperSeries:
GSE12466 Transcriptional signatures of Itk-deficient CD3+, CD4+ and CD8+ T-cells
Relations
BioProject PRJNA114227

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE12465_RAW.tar 55.6 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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