|
| Status |
Public on Jul 01, 2016 |
| Title |
CM115-normal |
| Sample type |
RNA |
| |
|
| Source name |
breast tissue adjacent to tumor
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: CM115N
tissue: normal
er: pos
her2: neg
cohort: cohort_1
age_in_years: 64
bmi: NA
tumor_size_cm: 2.5
array_scan_date: 2010-10-27
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were stabilized with RNAlater at the time of surgery. After surgery, RNAlater was removed and tissue was stored at -80°C. RNA was extracted with TRIzol (Invitrogen, Carlsbad CA) or TRI reagent (Life Technologies, Gaithersburg MD) and further purified on RNeasy columns in combination with the RNeasy Mini Kit (Qiagen, Valenca, CA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington DE) and quality checked with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5
|
| |
|
| Hybridization protocol |
Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5
|
| Scan protocol |
Scanning on Agilent scanner G2505B
|
| Description |
CM115N
gene expression from breast tissue adjacent to tumor
|
| Data processing |
Expression data were background-corrected and quantile normalized using limma in R. Features flagged as non-uniform or below-background were excluded. Batch effect from Scan Date was corrected using ComBat.
|
| |
|
| Submission date |
Jul 14, 2015 |
| Last update date |
Jul 01, 2016 |
| Contact name |
David Quigley |
| Organization name |
UCSF
|
| Department |
Helen Diller Comprehensive Cancer Center
|
| Lab |
Ashworth Lab
|
| Street address |
1450 Third St. Room 207
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE70905 |
Age and estrogen-dependent inflammation in breast adenocarcinoma and normal breast tissue [cohort_1] |
| GSE70951 |
Paired Breast Adenocarcinoma and Adjacent Normal tissue |
|
