|
| Status |
Public on Sep 01, 2015 |
| Title |
EtOH_Untr_ctrl |
| Sample type |
RNA |
| |
|
| Source name |
Chronic ethanol-fed liver, untreated, prior to PHx
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain/background: Sprague-Dawley
gender: male
tissue: liver
diet: ethanol
treatment: none
timepoint: 0 (control)
animal ids: 375, 377, 379, 381
|
| Treatment protocol |
Rats received i.p. injection of AM21 (7.5 mg/kg) in saline (1 ml) 72 h prior to PHx and the second injection immediately following PHx. Liver tissue was freeze-clamped in liquid nitrogen at the time of PHx and 24 h after PHx. Tissue was then stored at -80 degrees C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Animal Tissue RNA Purification Kit (Norgen Biotek) and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100. RNA from 3 (AM21 treated samples) or 4 (untreated samples) biological replicates were pooled.
|
| Label |
Biotin
|
| Label protocol |
50 ng of total RNA was reverse transcribed using a chimeric cDNA/mRNA primer, and a second complementary cDNA strand was synthesized. Purified cDNA was then amplified with ribo-SPIA enzyme and SPIA DNA/RNA primers (NuGEN Technologies, San Carlos, CA). Amplified cDNA was purified with Qiagen MinElute reaction cleanup kit. 5 μg of cDNAs were fragmented and chemically labeled with biotin to generate biotinylated cDNA using FL-Ovation cDNA biotin module (NuGen Technologies).
|
| |
|
| Hybridization protocol |
Rat Gene 2.0 ST Array were hybridized with 5 μg of fragmented and biotin-labeled cDNA in 220 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h. Arrays were then washed and stained using GeneChip Fluidic Station 450, using Affymetrix GeneChip Hybridization, Wash & Stain Kit.
|
| Scan protocol |
Chips were scanned on an Affymetrix GeneChip Scanner 3000 7G, using Command Console Software.
|
| Description |
Untr_EtOH_LLM
Gene expression in chronic ethanol-fed liver prior to partial hepatectomy.
|
| Data processing |
Raw gene expression data was normalized using RMA in Affymetrix Expression Console.
|
| |
|
| Submission date |
Mar 24, 2015 |
| Last update date |
Sep 01, 2015 |
| Contact name |
Egle Juskeviciute |
| Organization name |
Thomas Jefferson University
|
| Department |
Pathology
|
| Street address |
1020 Locust st. JAH 527
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL17117 |
| Series (1) |
| GSE67242 |
Analysis of the role of miR-21 in liver regeneration after partial hepatectomy (PHx) in chronic ethanol-treated rats through in vivo inhibition using LNAs |
|
