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Sample GSM952008 Query DataSets for GSM952008
Status Public on Jul 01, 2012
Title AND.Rag1-/-H-2d DP thymocytes_MCC/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: MCC/I-Ek
protocol: negative 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 of pre-selected DP thymocytes from MCC/I-Ek stimulation (negative selection signals)
SAMPLE 1
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
ID_REF
VALUE dChip signal
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 4276.25 0
ILMN_2721178 1049.969 0
ILMN_3033922 291.5646 0
ILMN_3092673 1094.54 0
ILMN_2816356 56.01011 0.01378446
ILMN_2808939 939.4169 0
ILMN_2634564 620.2593 0
ILMN_2737647 -3.519195 0.4874687
ILMN_2734484 187.1078 0
ILMN_2952292 81.39588 0.003759399
ILMN_2699078 -7.683574 0.622807
ILMN_1213681 308.7719 0
ILMN_2735413 -14.99396 0.8483709
ILMN_2735415 23.08609 0.0952381
ILMN_2891688 905.3364 0
ILMN_2637698 1358.313 0
ILMN_2674228 481.6927 0
ILMN_2601546 40.79295 0.03258145
ILMN_1230831 -19.2255 0.9360902
ILMN_2848071 31.66504 0.05513784

Total number of rows: 25697

Table truncated, full table size 755 Kbytes.




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

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