|
| Status |
Public on Jun 25, 2013 |
| Title |
9830-010255B NEW PROTOCOL V5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Human Reference
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Whole human total RNA
|
| Biomaterial provider |
Perou Lab-UNC-CH
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy Kit
|
| Label |
Cy3
|
| Label protocol |
described in Hu et al., 2005, BioTechniques, 38:121-124
|
| |
|
| Channel 2 |
| Source name |
9830-010255B NEW PROTOCOL V5
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Tumor
age at diagnosis: 49
menopause status: NA
histopathology: NA
breast cancer subtype (pam50): Her2
er status: 0
hormone treated: NA
her2 status: 1
tumor grade: 3
tumor stage (t): 2
overall survival event (dead=1, alive=0): 0
overall survival (months): 47
|
| Biomaterial provider |
Perou Lab-UNC-CH
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy Kit
|
| Label |
Cy5
|
| Label protocol |
described in Hu et al., 2005, BioTechniques, 38:121-124
|
| |
|
| |
| Hybridization protocol |
described in Hu et al., 2005, BioTechniques, 38:121-124
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with a Agilent fluorescent scanner and image intensity data were extracted and analyzed with Agilent analysis software.
|
| Description |
Tumor sample
|
| Data processing |
Data for both channels were Lowess-normalized and then log(2) ratio was taken
|
| |
|
| Submission date |
Dec 12, 2011 |
| Last update date |
Jul 17, 2015 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
cperou@med.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
|
| Street address |
12-044 Lineberger Comprehensive Cancer Center CB# 7295
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL8269 |
| Series (3) |
| GSE34412 |
A Renewable Tissue Resource of Phenotypically Stable, Biologically and Ethnically Diverse, Patient-derived Human Breast Cancer Xenografts |
| GSE41119 |
Molecular Characterization of Basal-like and Non-Basal-like Triple-Negative Breast Cancers |
| GSE46604 |
Xenografting of advanced stage breast cancer preserves the genomic and clonal architecture and captures luminal tumors harboring mutations and gene rearrangements in ESR1 |
|
| Data table header descriptions |
| ID_REF |
Spot Reference ID |
| VALUE |
log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN) |
| SPOT |
spot number on array |
| CH1_MEAN |
|
| CH1_SD |
standard deviation of channel 1 intensity |
| CH1_BKD_MEDIAN |
channel 1 background median intensity |
| CH1_BKD_SD |
standard deviation of channel 1 background median intensity |
| CH2_MEAN |
channel 2 mean intensity |
| CH2_SD |
standard deviation of channel 2 intensity |
| CH2_BKD_MEDIAN |
channel 2 background median intensity |
| CH2_BKD_SD |
standard deviation of channel 2 background median intensity |
| TOT_BPIX |
number of background pixels |
| TOT_SPIX |
number of spot pixels |
| CH2BN_MEDIAN |
channel 2 normalized background median intensity |
| CH2IN_MEAN |
channel 2 normalized mean intensity |
| CH1DL_MEAN |
channel 1 Lowess_normalized mean intensity |
| CH2DL_MEAN |
channel 2 Lowess_normalized mean intensity |
| LOG_RAT2N_MEAN |
log2_ratio of channel 2 normalized over channel 1 (global normalization) |
| CORR |
correlation coefficient among pixels |
| FLAG |
Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots |
