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Sample GSM1334718 Query DataSets for GSM1334718
Status Public on Oct 27, 2014
Title E3 hom 4h
Sample type RNA
Source name T cells 4h stimulated
Organism Mus musculus
Characteristics strain: B6.C-Tg(CMV-cre)1Cgn/J
genotype: Malt1-/-
period of stimulation: 4h
treatment: stimulated
cell type: T cells
Treatment protocol Purification and stimulation of T-cells. Total T-cells were purified by negative selection using magnetic beads (Dynal, Invitrogen) against B cells (B220) and myeloid cells (CD11b). CD4+ T-cells were purified using MACS CD4+ or CD4+CD62L+ T Cell isolation kits (Miltenyi). Cells were stimulated with PMA (Adipogen) and ionomycin (Alexis) or with plate-bound anti-CD3 (145-2C11) and anti-CD28 (37.51, both eBioscience) antibodies after pre-coating with anti-Syrian hamster antibodies (F(ab')2 fragment of IgG H+L, rabbit, Jackson ImmunoResearch) at given concentrations and for indicated time points at 37°C.
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol applied for Illumina HiScan
Description KO homozygous
replicate 1
Data processing The data were normalised using quantile normalisation with Illumina Genomestudio 2011.1
Submission date Feb 26, 2014
Last update date Oct 27, 2014
Contact name Martin Irmler
Organization name Helmholtz Zentrum München GmbH
Department Institute of Experimental Genetics
Lab Gene Regulation & Epigenetics
Street address Ingolstaedter Landstrasse 1
City Neuherberg
State/province Bayern
ZIP/Postal code 85764
Country Germany
Platform ID GPL6885
Series (1)
GSE55360 Uncoupling Malt1 threshold function from paracaspase activity results in destructive autoimmune inflammation

Data table header descriptions
VALUE quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 770.5378 0
ILMN_2721178 172.5533 0
ILMN_3033922 134.2541 0
ILMN_3092673 473.3843 0
ILMN_2816356 3.678782 0.1328321
ILMN_2808939 269.7964 0
ILMN_2634564 202.1526 0
ILMN_2737647 1.296616 0.3182957
ILMN_2734484 21.73555 0
ILMN_2952292 32.25112 0
ILMN_2699078 0.1971482 0.4335839
ILMN_1213681 92.96639 0
ILMN_2735413 0.2140187 0.4335839
ILMN_2735415 0.1804284 0.4360902
ILMN_2891688 387.7162 0
ILMN_2637698 432.1555 0
ILMN_2674228 212.1359 0
ILMN_2601546 5.90767 0.05012531
ILMN_1230831 0.7950537 0.3721805
ILMN_2848071 3.691863 0.131579

Total number of rows: 25697

Table truncated, full table size 743 Kbytes.

Supplementary data files not provided
Processed data included within Sample table
Raw data are available on Series record

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