|
| Status |
Public on Jun 07, 2024 |
| Title |
patient 4 |
| Sample type |
RNA |
| |
|
| Source name |
macrodissected primary breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: macrodissected primary breast tumor
subject: S004
type of surgery: Lumpectomy
histology: IDC
er status: Negative
pr status: Negative
her2 status: Positive
pt: 1
pn: 0
ptnm: 1
radiotherapy: Yes
type of radiotherapy: Partial breast irradiation
age at diagnosis: 57.2484599589322
age at diagnosis (dichotomized): <65
race: White
chemotherapy: Yes
locoregional recurrence: No
death: Alive
time to locoregional recurrence from date of diagnosis (years): --
time to death or censor from date of diagnosis (years): 10.117808219178
bioanalyzer rin (rna integrity number): 8.7
|
| 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. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.
|
| Label |
biotin
|
| Label protocol |
Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.
|
| |
|
| 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.
|
| Data processing |
IRON normalization was performed on the dataset, batch corrected for RNA quality using PLS
|
| |
|
| Submission date |
Mar 28, 2022 |
| Last update date |
Jun 07, 2024 |
| Contact name |
Eric Welsh |
| E-mail(s) |
eric.welsh@moffitt.org
|
| Organization name |
H Lee Moffitt Cancer Center
|
| Department |
Biostatistics and Bioinformatics
|
| Street address |
12902 Magnolia Dr
|
| City |
Tampa |
| State/province |
FL |
| ZIP/Postal code |
33612 |
| Country |
USA |
| |
|
| Platform ID |
GPL15048 |
| Series (1) |
| GSE199633 |
Gene expression data for 637 human primary breast tumors with recurrence, ER/PR/HER2 status, and overall survival |
|
