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Sample GSM1028057 Query DataSets for GSM1028057
Status Public on Jun 11, 2013
Title C57BL/6J_XX_E11.6_gonad_rep2
Sample type RNA
 
Source name C57BL/6J, XX, E11.6 Gonad
Organism Mus musculus
Characteristics strain: C57BL/6J
Sex: XX
Stage: E11.6
Extracted molecule total RNA
Extraction protocol Total RNA was first extracted from individual pairs of E11.0-E12.0 XX and XY gonads (separated from mesonephroi) with the RNeasy Micro kit with on-column DNase digestion (QIAGEN, cat no. 74004) following the manufacturer’s protocol. Total RNA was eluted in 14 ul RNase-free water (not DEPC- treated), and 2 ul were used to quantify RNA concentration on a NanoDrop ND-2000 (Thermo Scientific). Only samples with > 100 ng of total RNA and an A280:A260 ratio of >1.6 were included in the expression analyses.
Label biotin
Label protocol From each total RNA sample, mRNA was selectively reverse transcribed with oligo(dT) primers to T7-labelled cDNA, and then amplified by in vitro transcription (IVT) to produce biotinylated cRNA using the Illumina TotalPrep Amplification Kit (Ambion/ Life Technologies, cat no. AMIL1791) according to manufacturer’s instructions.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description replicate 2
Data processing The data were normalised using quantile normalisation with BeadArray,a package in BioConductor, in R [version of R 2.12.0 and beadarray version 2.0.6].
 
Submission date Oct 31, 2012
Last update date Jun 11, 2013
Contact name Anirudh Natarajan
Organization name Duke University Medical Center
Lab Blanche Capel
Street address 4034 GSRBII Building, Research Drive
City Durham
State/province NC
ZIP/Postal code 27705
Country USA
 
Platform ID GPL6885
Series (1)
GSE41948 Fine Time-Course Expression Analysis of Mammalian Sex Determination in 129S1/SvImJ and C57BL/6J XX and XY mice

Data table header descriptions
ID_REF
VALUE quantile normalized and log2 transformed
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 11.81921859 0
ILMN_2721178 9.489210137 0
ILMN_3033922 9.030424312 0
ILMN_3092673 10.81726627 0
ILMN_2816356 7.472598706 0.03383
ILMN_2808939 10.23659829 0
ILMN_2634564 9.462642228 0
ILMN_2737647 7.212798534 0.32707
ILMN_2734484 8.91550727 0
ILMN_2952292 7.695065244 0.00251
ILMN_2699078 7.073341211 0.7406
ILMN_1213681 8.723577683 0
ILMN_2735413 7.368319993 0.1015
ILMN_2735415 7.228765558 0.29323
ILMN_2891688 10.01359281 0
ILMN_2637698 9.801808674 0
ILMN_2674228 9.208914111 0
ILMN_2601546 7.356870143 0.10652
ILMN_1230831 7.333970194 0.13158
ILMN_2848071 7.048751777 0.80952

Total number of rows: 25697

Table truncated, full table size 773 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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