{"owner": "ArrayExpress Uploader", "pop_total": 0, "species": "mouse", "factors": [{"GSE12465GSM313189": {}}, {"GSE12465GSM313190": {}}, {"GSE12465GSM313191": {}}, {"GSE12465GSM313192": {}}, {"GSE12465GSM313193": {}}, {"GSE12465GSM313194": {}}, {"GSE12465GSM313195": {}}, {"GSE12465GSM313196": {}}, {"GSE12465GSM313197": {}}, {"GSE12465GSM313198": {}}, {"GSE12465GSM313199": {}}, {"GSE12465GSM313200": {}}, {"GSE12465GSM313201": {}}, {"GSE12465GSM313202": {}}], "id": 5457, "ownerprofile_id": "arrayexpress_sid", "platform": 6, "summary_wrapped": "The Tec-family kinase Itk plays an important role during T-cell activation and function, and controls also conventional versus innate-...", "geo_gse_id": "E-GEOD-12465", "owner_profile": "/profile/8773/arrayexpressuploader", "factor_count": 0, "sample_count": 14, "tags": ["cell", "chromatin", "lymph", "spleen"], "lastmodified": "Dec.12, 2014", "is_default": false, "geo_gds_id": "", "slug": "transcription-profiling-of-mouse-itk-deficienct-cd", "geo_id_plat": "E-GEOD-12465_A-AFFY-45", "name": "Transcription profiling of mouse Itk-deficienct CD3+, CD4+ and CD8+ T cells", "created": "Nov.10, 2014", "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. Experiment 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.", "source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-12465", "sample_source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-12465/samples/"}