|
| Status |
Public on Sep 10, 2011 |
| Title |
mammary tumor WT |
| Sample type |
RNA |
| |
|
| Source name |
Wild-type group, treated with MP-DMBA maintained on standard rodent chow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mammary tumor
genetic background: C57BL/6
genotype: wild type
treatment: MP-DMBA
|
| Treatment protocol |
Mice were maintained on standard rodent chow and injected s.c. with 15 mg MP suspension (Depo-Provera™), followed by four weekly doses of 1 mg DMBA/0.1 ml cottonseed oil administered by gavage
|
| Growth protocol |
All animal studies were conducted under GUACUC protocol 09-061. Female nulliparious Sca-1-knockout mice and age-matched C57/wild-type littermates were used in this study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mammary gland tissue was excised and preserved in RNAlater (Ambion) at -20◦C until RNA extraction using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed by an A260/A280 ratio of >1.9, and RNA quality was monitored using a microfluidic nanochip (Agilent). Each cRNA was prepared from equal amounts of RNA (1ug) pooled from 5 mice per group according to the manufacturers protocol (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
Biotin-labelled cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Biotin-labeled cRNA was fragmented at 94°C for 35 min and used for hybridization overnight to an Affymetrix mouse 430A2.0 GeneChip® by the Genomics and Epigenomics Shared Resource, LCCC, Georgetown University.
|
| Scan protocol |
The GeneChip® was scanned using an Agilent Gene Array scanner.
|
| Description |
Gene expression data from MP-DMBA induced mammary tumor in WT mice
|
| Data processing |
Raw data generation was performed with the Affymetrix GeneChip®ware 1.1. A noise value (Q) based on the variance of low-intensity probe cells was used to calculate a minimum threshold for each GeneChip. Data generated after scanning was subjected to comparison analysis to select change calls at 100% increase or decrease compared with control for each gene. Genes with a signal <300 in all experimental groups were excluded from subsequent analysis.
|
| |
|
| Submission date |
Sep 07, 2011 |
| Last update date |
Sep 10, 2011 |
| Contact name |
Robert I Glazer |
| E-mail(s) |
glazerr@georgetown.edu
|
| Phone |
202-687-8324
|
| URL |
http://explore.georgetown.edu/people/glazerr/?PageTemplateID=208
|
| Organization name |
Georgetown University
|
| Department |
Oncology
|
| Street address |
3970 Reservoir Rd, NW
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20007 |
| Country |
USA |
| |
|
| Platform ID |
GPL8321 |
| Series (1) |
| GSE31954 |
Expression data from Sca-1 knockout mice |
|
