|
| Status |
Public on Sep 27, 2013 |
| Title |
wild-type DEN tumor #2 |
| Sample type |
RNA |
| |
|
| Source name |
liver tumor RNA 9 months old
|
| Organism |
Mus musculus |
| Characteristics |
gender: male
strain: C57BL/6J
genotype: wild-type
tissue: liver tumor
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 |
|
