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Sample GSM952009 Query DataSets for GSM952009
Status Public on Jul 01, 2012
Title AND.Rag1-/-H-2d DP thymocytes_gp250/I-Ek stimulation_rep1
Sample type RNA
Source name Pre-selected DP thymocytes from AND.Rag1-/-H-2d mouse
Organism Mus musculus
Characteristics cell type: Pre-selected DP thymocyte
genotype/variation: AND.Rag1-/-H-2d
agent: gp250/I-Ek
protocol: positive selection signals
Treatment protocol 1x106 thymocytes were stimulated with plate bound peptide loaded I-Ek Ig dimers for seven hours
Growth protocol Pre-selected thymocytes were cultured in Iscove's DMEM containing 10% FCS, 1x nonessential amino acid, 2 mM GlutaMax, 1 mM sodium pyruvate, 0.05% gentamicin, 50 ┬ÁM 2-mercaptoethanol
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Rneasy kits (Qiagene) according to the manufacturer's instructions
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
Description Gene expression data from pre-selected DP cells from gp250/I-Ek stimulation (positive selection signals)
Data processing Data was normalized and modeled using dChip software.
Submission date Jun 25, 2012
Last update date Jul 01, 2012
Contact name Wan-Lin Lo
Organization name Washington University in St Louis
Street address 425 S Euclid Ave, campus box 8118
City Saint Louis
ZIP/Postal code 63110
Country USA
Platform ID GPL6885
Series (1)
GSE38909 Transcriptional profiling analysis of pre-selected DP thymocytes in response to positive and negative selection signals

Data table header descriptions
VALUE dChip signal
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 4670.511 0
ILMN_2721178 1221.854 0
ILMN_3033922 584.7877 0
ILMN_3092673 2496.314 0
ILMN_2816356 53.88958 0.02255639
ILMN_2808939 496.2328 0
ILMN_2634564 272.2701 0
ILMN_2737647 6.540501 0.2869674
ILMN_2734484 381.1924 0
ILMN_2952292 63.69599 0.01002506
ILMN_2699078 -12.73163 0.7393484
ILMN_1213681 432.8597 0
ILMN_2735413 -14.08707 0.7781955
ILMN_2735415 33.04053 0.0651629
ILMN_2891688 524.1534 0
ILMN_2637698 3262.285 0
ILMN_2674228 474.6866 0
ILMN_2601546 16.59268 0.1466165
ILMN_1230831 -10.72464 0.6804512
ILMN_2848071 8.548234 0.2418546

Total number of rows: 25697

Table truncated, full table size 751 Kbytes.

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

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