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Sample GSM599941 Query DataSets for GSM599941
Status Public on Dec 22, 2010
Title C57BL/6J Oct4-EGFP+ cells_3
Sample type RNA
 
Source name germ cells
Organism Mus musculus
Characteristics strain: C57BL/6J
developmental stage: embryo
age: E14.5
gender: XY
tissue: embryonic male gonads
cell type: germ cells
testicular teratoma susceptibility: resistant
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 B6-3
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)
B6-3.Avg_NBEADS
B6-3.BEAD_STDERR
B6-3.Detection Pval

Data table
ID_REF VALUE B6-3.Avg_NBEADS B6-3.BEAD_STDERR B6-3.Detection Pval
ILMN_2896528 1819.689 51 83.56285 0
ILMN_2721178 374.068 39 24.55005 0
ILMN_3033922 252.9111 62 14.68871 0
ILMN_3092673 1059.999 40 37.30124 0
ILMN_2816356 31.39363 31 6.835894 0.003759399
ILMN_2808939 980.1577 49 41.68309 0
ILMN_2634564 582.8871 32 34.97673 0
ILMN_2737647 -9.430612 33 3.977579 0.8909774
ILMN_2734484 151.7443 27 14.44328 0
ILMN_2952292 49.10754 48 6.553012 0
ILMN_2699078 -2.715903 42 4.774605 0.5952381
ILMN_1213681 165.0424 40 10.8989 0
ILMN_2735413 9.307959 30 6.879178 0.1278196
ILMN_2735415 -2.928104 38 4.099227 0.5977443
ILMN_2891688 180.4044 35 15.68837 0
ILMN_2637698 368.8346 53 18.30427 0
ILMN_2674228 1038.206 43 61.33285 0
ILMN_2601546 -4.119505 36 4.095687 0.6741855
ILMN_1230831 -4.294278 34 4.096511 0.6829574
ILMN_2848071 -2.124338 21 4.052746 0.5551379

Total number of rows: 25697

Table truncated, full table size 1037 Kbytes.




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

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