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Sample GSM1240336 Query DataSets for GSM1240336
Status Public on Sep 27, 2013
Title Chop-/- PBS #1
Sample type RNA
 
Source name whole liver RNA 9 months old
Organism Mus musculus
Characteristics gender: male
strain: C57BL/6J
genotype: Chop-/-
tissue: whole liver
treatment: PBS
Extracted molecule total RNA
Extraction protocol Resected livers or liver tumors were flash frozen in liquid nitrogen. Total RNA was extracted from frozen material using Trizol.
Label Biotin
Label protocol 100 nanograms total RNA was converted to amplified Biotin-aRNA using the Epicentre TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Illumina, Inc., San Diego, CA, Cat. #TAN07924) according to the manufacturer’s recommended protocol. The amplified Biotin-aRNA product was purified through a QIAGEN RNeasy MinElute Cleanup column (QIAGEN Cat #74204) according to modifications from Epicentre.
 
Hybridization protocol 750ng of this product were mixed with Illumina hybridization buffer, placed onto Illumina mouseRef8 v2 BeadChips (Part No. BD-202-0202), and incubated at 58º C for 17h, with rocking, in an Illumina Hybridization Oven. Following hybridization, the arrays were washed, blocked, then stained with streptavidin-Cy3 (Amersham/GE Healthcare, Piscataway, NJ) according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay protocol.
Scan protocol Beadchips were scanned with the Illumina iScan System (ID #N054)
Data processing Data were collected using the GenomeStudio software v2011.1. Default parameters within GenomeStudio were used.
 
Submission date Sep 26, 2013
Last update date Sep 27, 2013
Contact name David Thomas Rutkowski
E-mail(s) thomas-rutkowski@uiowa.edu
Organization name University of Iowa Carver College of Medicine
Department Anatomy and Cell Biology
Street address 51 Newton Rd.
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
 
Platform ID GPL6885
Series (1)
GSE51188 The Stress-Regulated Transcription Factor CHOP Promotes Hepatic Inflammatory Gene Expression, Fibrosis, and Oncogenesis

Data table header descriptions
ID_REF
VALUE GenomeStudieo v. 2011.1 (Gene Expression Module 1.9.0) quantile normalized data were exported using the Partex plugin version 2.16 as log(2) expression values.

Data table
ID_REF VALUE
ILMN_2896528 10.8093
ILMN_2721178 8.43994
ILMN_3033922 9.0022
ILMN_3092673 12.1306
ILMN_2816356 6.93324
ILMN_2808939 9.95133
ILMN_2634564 9.29321
ILMN_2737647 6.81225
ILMN_2734484 9.2572
ILMN_2952292 7.90631
ILMN_2699078 6.63137
ILMN_1213681 8.48052
ILMN_2735413 9.2218
ILMN_2735415 9.37582
ILMN_2891688 9.20706
ILMN_2637698 9.03776
ILMN_2674228 7.84151
ILMN_2601546 6.71553
ILMN_1230831 6.74869
ILMN_2848071 9.97083

Total number of rows: 25697

Table truncated, full table size 524 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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