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Sample GSM456187 Query DataSets for GSM456187
Status Public on May 12, 2010
Title P2-1
Sample type RNA
 
Source name Passage 2 cells
Organism Mus musculus
Characteristics strain: Pten Loxp/loxp;Alb-Cre
genome/variation: Liver-specific Pten deletion
tissue: liver
cell type: liver tumor cells
cell passage: 2
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.
Label Cy3
Label protocol Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Replicate 1
Data processing Raw data was extracted from Illumina's Beadstudio v3.0. Normalization was done in Beadstudio v.3 using the Average Normalization method. The data were then converted to t16 log2 ratios. This was done to generate sufficient number of data points for a one sample t-test (4 replicates for each sample; 4x4). One sample t-test was performed using Tigr MEV v4.4 with p<0.05. Probe sets with at least a 1.4 fold were considered for the final candidate gene list.
 
Submission date Sep 24, 2009
Last update date May 12, 2010
Contact name Wei Ding
Organization name Pennsylvania State University College of Medicine
Department Pediatrics
Lab Rountree Lab
Street address 500 University Drive
City Hershey
State/province PA
ZIP/Postal code 17033
Country USA
 
Platform ID GPL6885
Series (1)
GSE18255 Epithelial-to-Mesenchymal Transition of Murine PTEN-/- Liver Tumor Cells Promotes Tumor Growth and Invasion

Data table header descriptions
ID_REF
VALUE Beadstudio 3.0 normalized log 2 transformed signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1248788 4.904691215 0.9716859
ILMN_2707227 5.47667104 0
ILMN_2896528 10.52814444 0
ILMN_2721178 8.688065283 0
ILMN_1227723 7.162099235 0
ILMN_3033922 8.366737913 0
ILMN_3092673 10.10156735 0
ILMN_2730714 11.58503623 0
ILMN_3162224 9.576173288 0
ILMN_2816356 5.649981547 0
ILMN_2808939 8.566368428 0
ILMN_2634564 7.93143132 0
ILMN_1216623 8.38102894 0
ILMN_1215157 8.939547187 0
ILMN_1228777 4.898646126 0.978121
ILMN_2737647 5.122688454 0.3359073
ILMN_1216425 5.016192755 0.6859717
ILMN_2734484 7.492835397 0
ILMN_2652961 5.008191496 0.7129987
ILMN_2952292 5.905646216 0

Total number of rows: 25697

Table truncated, full table size 784 Kbytes.




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

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