|
| Status |
Public on Jun 19, 2014 |
| Title |
Breast tumor 398 |
| Sample type |
RNA |
| |
|
| Source name |
Human primary breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
age: 61
margin (cm): 0.5
tumor type: IDC
tumor size (cm): 3.1
tumor grade: 3
ln positive (total): 0 (4)
lvi: No
eic: No
er: Negative
pr: Negative
her2: Positive
cmtc: 3
recurrence: no
recurrence free time (months): 30.40
location of recurrence: no
used in the 284bc dataset?: yes
rin: 6.8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from fine needle aspirates of tumors with QIAGEN RNAeasy Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.
|
| Label |
Biotin
|
| Label protocol |
200 ng of total RNA were converted to cDNA, followed by an in vitro transcription amplification step to generate biotin-labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit (Applied Biosystems, Austin, TX).
|
| |
|
| Hybridization protocol |
750 ng of labeled cRNA were applied to Illimuna whole-genome gene expression HumanRef-8 v2 BeadChips for an overnight hybridization at 58°C.
|
| Scan protocol |
Signal is developed with streptavidin-Cy3 and the BeadChip is scanned with the Illumina BeadArray Reader.
|
| Description |
5083888056_E: GP398
|
| Data processing |
Image data were processed by GenomeStudio software using background subtraction and quantile normalization. Methods to adjust the normalized intensity values see MAQC Consortium’s description [PMID: 16964229]. Log2 expression ratio of a normalized intensity value to the average signal in all samples for each transcript was calculated.
|
| |
|
| Submission date |
Apr 03, 2013 |
| Last update date |
Jun 19, 2014 |
| Contact name |
Dong-Yu Wang |
| Organization name |
UHN-PMH-OCI
|
| Street address |
610 University Ave
|
| City |
Toronto |
| ZIP/Postal code |
M5G 2M9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6883 |
| Series (1) |
| GSE45725 |
Internal validation cohort of breast cancers for development of ClinicoMolecular Triad Classification |
|
