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Sample GSM599939 Query DataSets for GSM599939
Status Public on Dec 22, 2010
Title C57BL/6J Oct4-EGFP+ cells_1
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 B6-1
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)
B6-1.Avg_NBEADS
B6-1.BEAD_STDERR
B6-1.Detection Pval

Data table
ID_REF VALUE B6-1.Avg_NBEADS B6-1.BEAD_STDERR B6-1.Detection Pval
ILMN_2896528 1326.296 46 78.71656 0
ILMN_2721178 271.6261 47 21.18269 0
ILMN_3033922 153.6939 44 16.4502 0
ILMN_3092673 811.5331 46 37.66294 0
ILMN_2816356 22.85724 34 12.28495 0.08145364
ILMN_2808939 863.52 45 53.62529 0
ILMN_2634564 695.7325 45 46.62098 0
ILMN_2737647 -23.66304 41 9.066854 0.952381
ILMN_2734484 180.2261 34 24.84265 0
ILMN_2952292 47.07745 41 11.35632 0.003759399
ILMN_2699078 -9.747022 45 9.577118 0.7218045
ILMN_1213681 182.2215 47 19.49087 0
ILMN_2735413 9.100475 37 12.08864 0.2719298
ILMN_2735415 -24.69649 37 7.328235 0.9598997
ILMN_2891688 74.54308 37 13.77941 0
ILMN_2637698 348.206 53 27.49388 0
ILMN_2674228 1006.271 51 54.27877 0
ILMN_2601546 13.30724 44 9.626209 0.2017544
ILMN_1230831 23.10175 35 14.79764 0.0802005
ILMN_2848071 -6.868622 27 9.786727 0.6441103

Total number of rows: 25697

Table truncated, full table size 1043 Kbytes.




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

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