|
Status |
Public on Sep 27, 2013 |
Title |
Chop-/- DEN #2 |
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: 25 mg/kg DEN
|
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 |
|