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Sample GSM1334719 Query DataSets for GSM1334719
Status Public on Oct 27, 2014
Title E4 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 2
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 962.8624 0
ILMN_2721178 253.977 0
ILMN_3033922 137.6949 0
ILMN_3092673 474.2668 0
ILMN_2816356 -1.317233 0.6077694
ILMN_2808939 277.5469 0
ILMN_2634564 141.6009 0
ILMN_2737647 -1.390144 0.6253133
ILMN_2734484 10.53543 0.0112782
ILMN_2952292 27.44966 0
ILMN_2699078 -4.329752 0.8609022
ILMN_1213681 77.58091 0
ILMN_2735413 0.1671236 0.452381
ILMN_2735415 -4.991358 0.8834587
ILMN_2891688 246.6204 0
ILMN_2637698 424.7422 0
ILMN_2674228 206.23 0
ILMN_2601546 8.058465 0.03258145
ILMN_1230831 0.7705054 0.3934837
ILMN_2848071 4.898799 0.0952381

Total number of rows: 25697

Table truncated, full table size 754 Kbytes.




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

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