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Sample GSM599942 Query DataSets for GSM599942
Status Public on Dec 22, 2010
Title 129S1/SvImJ Oct4-EGFP+ cells_1
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 129S1-1
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)
129S1-1.Avg_NBEADS
129S1-1.BEAD_STDERR
129S1-1.Detection Pval

Data table
ID_REF VALUE 129S1-1.Avg_NBEADS 129S1-1.BEAD_STDERR 129S1-1.Detection Pval
ILMN_2896528 1529.81 49 72.87878 0
ILMN_2721178 360.8283 39 29.26724 0
ILMN_3033922 292.6262 47 20.43614 0
ILMN_3092673 1439.526 53 50.41719 0
ILMN_2816356 21.32215 34 6.193086 0.01879699
ILMN_2808939 1067.91 48 45.81821 0
ILMN_2634564 531.2258 41 26.54863 0
ILMN_2737647 -0.6652902 32 5.18522 0.4937343
ILMN_2734484 128.5536 36 16.20618 0
ILMN_2952292 35.64546 41 6.120353 0.002506266
ILMN_2699078 4.497761 44 4.761487 0.2756892
ILMN_1213681 174.4765 49 10.28273 0
ILMN_2735413 3.29024 36 7.047536 0.3145363
ILMN_2735415 17.13103 44 6.404802 0.04010025
ILMN_2891688 164.2558 26 15.56462 0
ILMN_2637698 295.7265 42 15.84013 0
ILMN_2674228 908.2568 46 48.4232 0
ILMN_2601546 10.87783 31 4.655363 0.1090226
ILMN_1230831 16.34795 29 8.036676 0.04260652
ILMN_2848071 19.78107 38 6.227099 0.02130326

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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