|
| Status |
Public on May 03, 2019 |
| Title |
P6-2-Affy-FF |
| Sample type |
RNA |
| |
|
| Source name |
Breast cancer tissue.
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer
time point: early on-treatment biopsy
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from fresh frozen tissue using the Qiagen miRNeasy kit.
|
| Label |
Biotin
|
| Label protocol |
Approximately 500 ng of total RNA was processed to produce biotinylated cRNA targets.
|
| |
|
| Hybridization protocol |
As per standard Affymetrix protocol.
|
| Scan protocol |
As per standard Affymetrix protocol, using a GCS2500 scanner.
|
| Description |
Patient 6 early on-treatment biopsy sequenced using Affymetrix U133A technology from fresh frozen.
SAMPLE 2
|
| Data processing |
All statistical analyses were performed using the R/Bioconductor software (http://www.bioconductor.org/) unless stated otherwise. Preprocessing—the raw CEL files were preprocessed using robust multichip average methodology, which encompasses background correction, normalization, and summarization. Nonspecific filtering—using Affymetrix’ absolute call data, genes with “present” calls in fewer than 80% of arrays were discarded so reducing genes whose expression were largely in the noise range.
|
| |
|
| Submission date |
Apr 29, 2019 |
| Last update date |
May 04, 2019 |
| Contact name |
Carlos Martinez-Perez |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Edinburgh
|
| Department |
Institute of Genetics and Molecular Medicine
|
| Street address |
Western General Hospital, Crewe Road South
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE130459 |
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches [Affy_U133A] |
| GSE130645 |
Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: Comparison of gene expression profiling approaches |
|
