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Sample GSM599940 Query DataSets for GSM599940
Status Public on Dec 22, 2010
Title C57BL/6J Oct4-EGFP+ cells_2
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 B6-2
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)
B6-2.Avg_NBEADS
B6-2.BEAD_STDERR
B6-2.Detection Pval

Data table
ID_REF VALUE B6-2.Avg_NBEADS B6-2.BEAD_STDERR B6-2.Detection Pval
ILMN_2896528 1565.477 47 64.35739 0
ILMN_2721178 359.5491 48 22.86331 0
ILMN_3033922 251.2159 47 15.19646 0
ILMN_3092673 1027.243 39 50.11293 0
ILMN_2816356 25.31717 35 7.388463 0.007518797
ILMN_2808939 990.3755 39 58.31968 0
ILMN_2634564 563.6137 41 33.35946 0
ILMN_2737647 -8.906241 29 6.81279 0.8358396
ILMN_2734484 118.7475 28 14.33333 0
ILMN_2952292 65.58175 56 8.12531 0
ILMN_2699078 -1.533429 38 6.027816 0.5401003
ILMN_1213681 204.2867 38 16.21549 0
ILMN_2735413 -1.21018 36 6.122005 0.5225564
ILMN_2735415 -5.944858 39 4.642207 0.7280702
ILMN_2891688 205.5647 32 19.75397 0
ILMN_2637698 289.1099 41 20.10832 0
ILMN_2674228 946.3727 51 50.486 0
ILMN_2601546 11.84951 48 5.093802 0.09774436
ILMN_1230831 -19.37765 40 3.473611 0.9924812
ILMN_2848071 3.920941 28 4.783803 0.3157895

Total number of rows: 25697

Table truncated, full table size 1045 Kbytes.




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

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