|
| Status |
Public on Dec 09, 2019 |
| Title |
TNBC sample42 |
| Sample type |
RNA |
| |
|
| Source name |
TNBC 42 breast cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer
type: TNBC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
|
| Label |
Biotin
|
| Label protocol |
The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.
|
| |
|
| Hybridization protocol |
GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
|
| Scan protocol |
Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
|
| Description |
t@52070900905334053111410586109846
|
| Data processing |
Data were processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).
|
| |
|
| Submission date |
Nov 03, 2014 |
| Last update date |
Dec 09, 2019 |
| Contact name |
Douglas Marchion |
| E-mail(s) |
[email protected]
|
| Phone |
813-745-4849
|
| Organization name |
Moffitt Cancer Center
|
| Department |
Clinical Science Lab
|
| Lab |
Dr. Lancaster's lab
|
| Street address |
12902 Magnolia Drive
|
| City |
Tampa |
| State/province |
Florida |
| ZIP/Postal code |
33647 |
| Country |
USA |
| |
|
| Platform ID |
GPL15048 |
| Series (1) |
| GSE62931 |
Baseline expression profiles of human breast carcinomas |
|
