|
| Status |
Public on Jan 07, 2010 |
| Title |
UNC05-0364A |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Human Reference B
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
composition: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs
|
| Biomaterial provider |
Stratagene
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated by Stratagene.
|
| Label |
Cy3
|
| Label protocol |
Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).
|
| |
|
| Channel 2 |
| Source name |
Normal Tissue Adjacent to Breast Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: normal tissue adjacent to breast tumor
patient id: UNC050364
active or "inactive": positive
age at diagnosis (year): 67
menopause status: Post
histopathology: Invasive
breast cancer subtype (pam50): Normal-like
er status: positive
hormone treated: yes
her2 status: negative
tumor grade: 2
tumor size (cm): 2.2
overall survival event (dead=1, alive=0): 0
overall survival (month): 59
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Kit.
|
| Label |
Cy5
|
| Label protocol |
Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).
|
| |
|
| |
| Hybridization protocol |
Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.
|
| Description |
251976010076-244K
Agilent Catalog 4 by 44k whole genome array UNC05-0364A, TEST SET
|
| Data processing |
Data for both channels were Lowess-normalized using the University of North Carolina (UNC) microarray database, and then the log(2) ratio (test/reference) was taken.
|
| |
|
| Submission date |
May 14, 2009 |
| Last update date |
Oct 28, 2011 |
| Contact name |
Melissa Troester |
| E-mail(s) |
[email protected]
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Epidemiology
|
| Street address |
135 Dauer Drive, CB 7435
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL8269 |
| Series (2) |
| GSE16113 |
Activation of Host Wound Responses in Breast Cancer Microenvironment |
| GSE31589 |
Expression of Epithelial-to-Mesenchymal Transition (EMT)-associated genes in extratumoral microenvironment predicts poor clinical outcome in breast cancer patients |
|
| Data table header descriptions |
| ID_REF |
Spot Reference ID |
| VALUE |
log2_ratio of channel 2 Lowess_normalized over channel 1 |
| SPOT |
spot number on array |
| CH1_MEAN |
channel 1 mean intensity |
| 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 CH2DN_MEAN(CH2N_MEAN - CH2BN_MEDIAN) over CH1D_MEAN(CH1_MEAN - CH1BKD_MEDIAN) |
| CORR |
correlation coefficient among pixels |
| FLAG |
Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots |
