|
| Status |
Public on Oct 11, 2013 |
| Title |
embryonal RMS_Tumor 5 (eRMS) |
| Sample type |
RNA |
| |
|
| Source name |
P7KP mice injected with IP tamoxifen
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed 129 S4/SvJae x C57/Bl6
sarcoma derived from: Pax7+ cells
genotype: mutant Kras and loss of both alleles of p53 in Pax7+ cells
sarcoma/tumor: embryonal RMS (eRMS)
age: > 6 weeks old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor sections stabilized in RNAlater and RNA extracted by grinding in liquid nitrogen and use of the Qiagen RNEasy Micro kit. Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A [software: 2100 Expert B.02.08.SI648] (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer [software: NanoDrop 8000 2.1.0] (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to GeneChip® Mouse Genome 430A 2.0 arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip® Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).
|
| Label |
biotin
|
| Label protocol |
MessageAmp™ Premier RNA Amplification Kit (Part Number 4385821, AM1792, 4383452)
|
| |
|
| Hybridization protocol |
fluidic station: Affymetrix GeneChip® Fluidics Station 450 [software: Affymetrix GeneChip® Command Console Fluidics Control 3.0.0.1214], hybridization oven new: Affymetrix GeneChip® hybridization Oven 645
|
| Scan protocol |
Affymetrix GeneChip® Scanner 7G. Affymetrix GeneChip® Command Console Scan Control 3.0.0.1214, sample register: Affymetrix GeneChip® Command Console Portal 3.0.1.1229, image viewer: Affymetrix GeneChip® Command Console Viewer 3.0.0.1214
|
| Description |
Gene expression from sarcomas derived from Pax7+ cells
|
| Data processing |
Affymetrix Expression Console version 1.1
|
| |
|
| Submission date |
May 10, 2013 |
| Last update date |
Oct 11, 2013 |
| Contact name |
Jordan Blum |
| Organization name |
Duke University Medical Center
|
| Street address |
450 Research Dr LSRC RmB232
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL8321 |
| Series (1) |
| GSE46836 |
Expression data from murine sarcomas |
|
