|
| Status |
Public on Sep 02, 2010 |
| Title |
Expired U133A_B_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
MAQC sample B, i.e., Ambion Human Brain Reference RNA (HBRR, Catalog #6050)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain reference
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The two RNA samples had been stored under 80°C at their respective vendor’ freezer since 2005, and were shipped with dry ice from the vendors to the microarray laboratory of Dr. Charles Wang at UCLA. The same batches of the two samples as those used in the MAQC project in 2005 were used in this study. Upon receiving RNA samples in 2009, the microarray laboratory evaluated and confirmed their quality using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer. The RNA Integrity Number (RIN) for each sample was around 8.0.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA samples were prepared according to the standard Affymetrix GeneChip® protocol. One µg of total RNA from each sample, along with poly A spikes (labeling control), were converted to double-stranded cDNA with GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA). After second-strand synthesis, the cDNA was purified with the GeneChip® Sample Cleanup Module (Affymetrix).
|
| |
|
| Hybridization protocol |
The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the GeneChip® 3’-Amplification Reagent Kit for IVT Labeling (Affymetrix). The A260/A280 ratio and yield of each of the cRNAs were recorded. For each sample, 10 µg of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to a GeneChip® microarray for 16 hours at 45ºC.
|
| Scan protocol |
Following hybridization, all microarrays were washed and stained in an Affymetrix GeneChip® Fluidics Station. Stained microarrays were scanned with an Affymetrix GeneChip® Scanner 3000.
|
| Description |
Ambion Human Brain Reference RNA
|
| Data processing |
Quality checks and data analyses were carried out using Affymetrix GeneChip® Operating Software (GCOS) and Quality Reporter.
|
| |
|
| Submission date |
Aug 31, 2010 |
| Last update date |
Sep 01, 2010 |
| Contact name |
Leming Shi |
| E-mail(s) |
[email protected]
|
| Phone |
+86-18616827008
|
| Organization name |
Fudan University
|
| Department |
School of Life Sciences
|
| Lab |
Center for Pharmacogenomics
|
| Street address |
2005 Songhu Road
|
| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE23906 |
Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples |
|
