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Sample GSM1334720 Query DataSets for GSM1334720
Status Public on Oct 27, 2014
Title E5 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 3
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
ID_REF
VALUE quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 1005.47 0
ILMN_2721178 238.9596 0
ILMN_3033922 136.6398 0
ILMN_3092673 646.2091 0
ILMN_2816356 2.375358 0.2819549
ILMN_2808939 330.7928 0
ILMN_2634564 109.6616 0
ILMN_2737647 -1.542726 0.6729323
ILMN_2734484 22.31224 0.003759399
ILMN_2952292 44.31381 0
ILMN_2699078 1.64458 0.3471178
ILMN_1213681 111.0073 0
ILMN_2735413 -2.797807 0.7719298
ILMN_2735415 -3.397812 0.8157895
ILMN_2891688 221.1594 0
ILMN_2637698 455.9894 0
ILMN_2674228 292.6932 0
ILMN_2601546 5.480698 0.1165414
ILMN_1230831 8.628827 0.05513784
ILMN_2848071 4.758848 0.1353384

Total number of rows: 25697

Table truncated, full table size 758 Kbytes.




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

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