|
| Status |
Public on Nov 02, 2011 |
| Title |
MD66-T20 |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer tissue, patient MD66, RNAlater, 20 min ischemic time
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: MD66
stabilization: RNAlater
extra_cold_ischemic_time_min: 20
true_cold_ischemic_time_min: 66
passedqc: Y
rna_integrity_number (as reported by the agillent bioanalyzer): 6.4
rna_concentration_ngpul: 354.7
rna_260_280: 2.04
|
| Treatment protocol |
Fresh tissue surgical excision specimens from breast cancer collected at time of surgery. The tissue was then cut into pieces of 1-2 mm in a petri dish using a sterile blade, mixed, and divided into 8 equal portions. A portion was placed into 1.5 ml RNAlater RNA stabilization reagent (Ambion, Inc., Austin TX) at baseline and 20, 40, 60, 120, and 180 minutes thereafter, or snap frozen in dry ice in a pre-chilled sample vial at baseline and 40 minutes thereafter. The time that each tissue portion was placed into contact with RNAlater solution or in the pre-chilled vial was recorded. Samples were stored at -70°C until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tissue using Qiagen Rneasy columns
|
| Label |
biotin
|
| Label protocol |
A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA is required for cRNA synthesis.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX
|
| Data processing |
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
|
| |
|
| Submission date |
Oct 29, 2010 |
| Last update date |
Nov 02, 2011 |
| Contact name |
Christos Hatzis |
| E-mail(s) |
[email protected]
|
| Phone |
781-938-3830
|
| URL |
http://www.nuverabio.com
|
| Organization name |
Nuvera Biosciences
|
| Street address |
400 West Cummings Park, Suite 5350
|
| City |
Woburn |
| State/province |
MA |
| ZIP/Postal code |
01801 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE25011 |
Study for evaluating the effect of cold ischemic time and RNA stabilization method on RNA integrity and gene expression measurements |
|
