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Sample GSM1554568 Query DataSets for GSM1554568
Status Public on Mar 30, 2015
Sample type RNA
Source name Liver tissue
Organism Mus musculus
Characteristics genotype/variation: pedf knockout
strain: C57B6
gender: male
age: 7 months old
Treatment protocol mice were fed high fat diet, liver tissue were collected and immediately flash frozen for subsequent RNA extraction
Growth protocol mice were fed high fat diet for 7 months
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 Bioanalyser.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Data processing The data were normalised using 75 percentile shift normalisation using Genespring GX 12.6.1
Submission date Nov 25, 2014
Last update date Mar 30, 2015
Contact name Petr Protiva
Phone 230-932-5711
Organization name Yale University and VA CT Healthcare System
Street address 950 Campbell Avenue
City West Haven
ZIP/Postal code 06516
Country USA
Platform ID GPL6885
Series (1)
GSE63643 Pigment Epithelium-Derived Factor (PEDF) Inhibits Wnt/β-catenin Signaling in the Liver

Data table header descriptions
VALUE normalized by shift to 75 percentile, log transformation (log2), baseline transformation to median of all samples

Data table
ID_REF VALUE PValue_6033111104_G
ILMN_2607609 -0.47580338 1
ILMN_1238674 0.22491455 0.77569
ILMN_3062534 0.1134696 0.98872
ILMN_3140158 0.05475998 1
ILMN_2674533 0.2361579 1
ILMN_2680307 0.14931536 0.85589
ILMN_2935307 0.061542034 0.33083
ILMN_1215893 -0.00453949 1
ILMN_2910106 -0.07961035 1
ILMN_2732092 -0.040184975 1
ILMN_2603725 0 1
ILMN_2664884 0.18451262 0.99248
ILMN_3003575 0.051758766 0.38221
ILMN_1229397 0.11471033 0.57268
ILMN_1225873 0.07183552 0.75439
ILMN_2899591 -0.039271355 1
ILMN_2658355 -0.23476267 1
ILMN_2682763 0.13558578 0.87594
ILMN_2521511 0.16258001 0.89474
ILMN_2691286 0.045313835 0.599

Total number of rows: 25697

Table truncated, full table size 730 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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