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Sample GSM952013 Query DataSets for GSM952013
Status Public on Jul 01, 2012
Title AND.Rag1-/-H-2d DP thymocytes_Hb/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: Hb/I-Ek
protocol: non-selecting 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 of pre-selected DP thymocyts from Hb/I-Ek stimulation (non-selecting 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 4553.129 0
ILMN_2721178 1152.352 0
ILMN_3033922 620.0945 0
ILMN_3092673 2634.314 0
ILMN_2816356 59.69308 0.00877193
ILMN_2808939 532.025 0
ILMN_2634564 250.8123 0
ILMN_2737647 8.083185 0.2606516
ILMN_2734484 286.5997 0
ILMN_2952292 38.62037 0.04385965
ILMN_2699078 -13.7219 0.7706767
ILMN_1213681 389.5998 0
ILMN_2735413 -24.5473 0.9724311
ILMN_2735415 36.50295 0.04887218
ILMN_2891688 647.588 0
ILMN_2637698 2908.72 0
ILMN_2674228 443.1546 0
ILMN_2601546 38.11456 0.04511278
ILMN_1230831 -2.670764 0.4761905
ILMN_2848071 28.22717 0.07017544

Total number of rows: 25697

Table truncated, full table size 752 Kbytes.

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

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