|
| Status |
Public on Mar 03, 2016 |
| Title |
SF Rapamycin, bio rep 3b |
| Sample type |
RNA |
| |
|
| Source name |
Solt_Farber_Rapamycin
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: F344
tissue: Liver
gender: Male
animal model: Rats were given an i.p. injection of diethylnitrosamine (200mg/kg) on day 1. On day 14 rats were implanted i.p. with a 2.5mg 14-day time release 2-acetylaminofluorene pellet. On day 21 rats were given a 2/3 partial hepatectomy and a subcutaneous 21-day time release rapamycin (2.5mg/kg/day) pellet. Animals were euthanized on day 70 of the protocol.
tissue features: GSTP + Persistent Focal Lesions
treatment: mTOR inhibitor rapamycin
|
| Treatment protocol |
Liver was harvested and tissue fixed in 10% neutral buffered formalin. Fixed tissue was subsequently embedded in paraffin. Sections were stained with Arcturus Paradise Plus staining solution according to manufacturer's directions.Laser capture microdissection was performed to isolate regions of interest.
|
| Growth protocol |
All animals were housed under standard conditions with access to food and water ad libitum. Rodents were euthanized by exsanguination under isoflurane anesthesia.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from FFPE sections using Qiagen’s FFPE RNeasy Kit according to the manufacturer's directions.
|
| Label |
biotin
|
| Label protocol |
SensationPlus™ FFPE Amplification and WT Labeling Kit from Affymetrix was used according to the manufacturer's directions. 150 ng total RNA input, 25 ug in vitro transcribed RNA and 3.5 ug labeled dsDNA per sample was used for hybridization.
|
| |
|
| Hybridization protocol |
60 ul total hyb volume with 3.5 ug labeled dsDNA, 60 rpm 47 C for 17 h
|
| Scan protocol |
Wash/Stain protocol FS450_0007 was used for washing and staining of the rat Gene ST 1.0 arrays. Arrays were scanned using an Affymetrix GeneScanner 3000 7G
|
| Description |
Solt_Farber_Rapamycin_3b
Duplicate array on same RNA as 3a
|
| Data processing |
Partek Genomics Suite v6.6 was used. Differential gene expression was determined using RMA for normalization and ANOVA with contrast. Differentially regulated genes had an FDR corrected p-value <0.05
|
| |
|
| Submission date |
Sep 15, 2015 |
| Last update date |
Mar 03, 2016 |
| Contact name |
Jennifer Ann Sanders |
| E-mail(s) |
Jennifer_Sanders@brown.edu
|
| Organization name |
Rhode Island Hospital
|
| Department |
Pediatric Endocrinology
|
| Street address |
593 Eddy Street
|
| City |
Providence |
| State/province |
RI |
| ZIP/Postal code |
02903 |
| Country |
USA |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE73039 |
Persistent Effect of mTOR Inhibition on Preneoplastic Foci Progression and Gene Expression in a Rat Model of Hepatocellular Carcinoma |
|
