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Sample GSM952012 Query DataSets for GSM952012
Status Public on Jul 01, 2012
Title AND.Rag1-/-H-2d DP thymocytes_gp250/I-Ek stimulation_rep2
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 4396.489 0
ILMN_2721178 1089.362 0
ILMN_3033922 682.7095 0
ILMN_3092673 2552.045 0
ILMN_2816356 56.50628 0.0112782
ILMN_2808939 497.869 0
ILMN_2634564 287.2386 0
ILMN_2737647 15.98223 0.141604
ILMN_2734484 417.4813 0
ILMN_2952292 43.07233 0.02756892
ILMN_2699078 -15.21632 0.8521304
ILMN_1213681 336.4071 0
ILMN_2735413 -18.45796 0.9360902
ILMN_2735415 22.86669 0.08646616
ILMN_2891688 529.4158 0
ILMN_2637698 3549.411 0
ILMN_2674228 450.2144 0
ILMN_2601546 25.89368 0.07393484
ILMN_1230831 4.264658 0.3107769
ILMN_2848071 33.0617 0.04010025

Total number of rows: 25697

Table truncated, full table size 750 Kbytes.

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

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