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Sample GSM1169188 Query DataSets for GSM1169188
Status Public on Jun 23, 2014
Title Cdh1_P53_cKO_3
Sample type RNA
 
Source name Cdh1 and P53 double knock-out
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: Cdh1 and P53 double knock-out; Cdh1-, P53-
age: 2 months
gender: female
tissue: uterus
Treatment protocol Female mice were genotyped and necropsied at 2 month of age. Uterine tissues were homogenized with Trizol reagent at collection and stored at-80C.
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit according to manufacturer's instructions.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description P43
Data processing The data were processed in R (2.14.1) using limma (3.10.2) using the neqc function, which does a normexp background correction using negative control probes, quantile normalization using negative and positive control probes and log2 transformation.
 
Submission date Jun 19, 2013
Last update date Jun 23, 2014
Contact name Kanako Hayashi
E-mail(s) [email protected]
Organization name Washington State University
Department School of Molecular Biosciences
Street address BLS345, 1770 NE Stadium Way
City Pullman
State/province WA
ZIP/Postal code 99164
Country USA
 
Platform ID GPL6887
Series (1)
GSE48131 Ablation of Cdh1 and Trp53 in the uterus reveals novel mechanisms controlling tumor microenvironment in endometrial cancer.

Data table header descriptions
ID_REF
VALUE log2 neqc-normalized expression values
Detection.Pval

Data table
ID_REF VALUE Detection.Pval
ILMN_2417611 4.39993735453593 0.5117521
ILMN_2762289 4.59980421223277 0.150641
ILMN_2896528 11.9134148565248 0
ILMN_2721178 10.0497452823205 0
ILMN_2458837 4.42694426249925 0.4113248
ILMN_3033922 9.60018308107029 0
ILMN_3092673 11.7579987911269 0
ILMN_1230777 11.205601459786 0
ILMN_1246069 10.8848555248794 0
ILMN_1232042 4.25864274654426 0.974359
ILMN_1243193 9.69191822582875 0
ILMN_2524361 4.50610014780506 0.2446581
ILMN_1242440 4.4261157410805 0.4134615
ILMN_1233188 8.95083100678917 0
ILMN_2543688 11.4888449422941 0
ILMN_1259789 5.89204963268955 0.001068376
ILMN_2816356 5.010201590115 0.02991453
ILMN_1224596 6.5908270969365 0
ILMN_1233643 4.66667372636343 0.1089744
ILMN_2808939 9.99195041538131 0

Total number of rows: 45281

Table truncated, full table size 1654 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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