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Sample GSM599943 Query DataSets for GSM599943
Status Public on Dec 22, 2010
Title 129S1/SvImJ Oct4-EGFP+ cells_2
Sample type RNA
 
Source name germ cells
Organism Mus musculus
Characteristics strain: 129S1/SvImJ
developmental stage: embryo
age: E14.5
gender: XY
tissue: embryonic male gonads
cell type: germ cells
testicular teratoma susceptibility: susceptible
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from Oct4-EGFP+ sorted germ cell populations (C57BL/6J n=3, 129/SvJ n=2) using the RNeasy Micro kit (Qiagen #74004) with on-column DNase digestion according to manufacturer’s protocols.
Label Cy3
Label protocol Total RNA was reverse transcribed to cDNA and then transcribed in vitro into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion #AMIL1791) according to manufacturer’s protocols.
 
Hybridization protocol 750ng of biotin-labelled cRNA was hybridized to MouseRef-8 v2.0 Expression BeadChips (Illumina BD-202-0202) according to Illumina protocols.
Scan protocol BeadChips were scanned on the iScan BeadArray Reader (Illumina) following Illumina protocols.
Description 129S1-2
Data processing Raw probe level data was imported into GenomeStudio (Illumina) software, average normalized, and the background signal level was subtracted out. Genes that were not detected in at least one sample (detection p-value cutoff = 0.05) were removed from the analysis. The Illumina custom error model with false discovery rate (FDR) correction was applied to detect genes that were differentially expressed between strains. Expression differences were considered significant if the calculated Diffscore was ± 13 (equivalent to a p-value < 0.05).
 
Submission date Sep 24, 2010
Last update date Dec 22, 2010
Contact name Steven C Munger
E-mail(s) steven.munger@jax.org
Organization name The Jackson Laboratory
Lab Steven Munger
Street address 600 Main Street
City Bar Harbor
State/province ME
ZIP/Postal code 04609
Country USA
 
Platform ID GPL6885
Series (1)
GSE24340 Regulation of male germ cell cycle arrest and differentiation by DND1 is modulated by genetic background

Data table header descriptions
ID_REF
VALUE normalized signal intensity (average-normalized and background subtracted)
129S1-2.Avg_NBEADS
129S1-2.BEAD_STDERR
129S1-2.Detection Pval

Data table
ID_REF VALUE 129S1-2.Avg_NBEADS 129S1-2.BEAD_STDERR 129S1-2.Detection Pval
ILMN_2896528 1463.078 47 65.90857 0
ILMN_2721178 314.5978 51 21.76751 0
ILMN_3033922 218.0681 33 19.78775 0
ILMN_3092673 1611.975 50 57.97281 0
ILMN_2816356 22.52636 29 7.1049 0.01378446
ILMN_2808939 1151.932 43 53.65894 0
ILMN_2634564 496.7912 32 37.65335 0
ILMN_2737647 -1.354311 33 4.723348 0.5313283
ILMN_2734484 132.5949 45 14.488 0
ILMN_2952292 11.47631 44 4.036871 0.08270676
ILMN_2699078 -1.633038 37 5.093537 0.5451128
ILMN_1213681 179.085 39 15.97203 0
ILMN_2735413 11.41782 40 6.156335 0.0839599
ILMN_2735415 24.06016 22 10.60809 0.01378446
ILMN_2891688 187.075 35 16.28202 0
ILMN_2637698 469.5273 40 27.11015 0
ILMN_2674228 666.6348 38 23.87783 0
ILMN_2601546 14.59883 29 6.961534 0.05764411
ILMN_1230831 4.095017 24 6.940214 0.2857143
ILMN_2848071 10.04167 29 7.054584 0.1177945

Total number of rows: 25697

Table truncated, full table size 1033 Kbytes.




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

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