|
| Status |
Public on Oct 21, 2013 |
| Title |
NCI10043 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Human Reference B
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
|
| Biomaterial provider |
Stratagene
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy Mini
|
| Label |
Cy3
|
| Label protocol |
described in Hu et al., 2005, BioTechniques, 38:121-130
|
| |
|
| Channel 2 |
| Source name |
Normal Tissue Adjacent to Breast Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
mammographic density: >=25%
mammographic dense area: >=median (36.52cm2)
microenvironment subtype: Inactive;Stromal proportion_tertile2;Epithelial proportion_tertile3;Adipose proportion_tertile2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy Mini
|
| Label |
Cy5
|
| Label protocol |
described in Hu et al., 2005, BioTechniques, 38:121-135
|
| |
|
| |
| Hybridization protocol |
described in Hu et al., 2005, BioTechniques, 38:121-135
|
| 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 |
Normal Tissue Adjacent to Breast Tumor
|
| Data processing |
Data for both channels were Lowess-normalized and then log(2) ratio was taken
|
| |
|
| Submission date |
Jul 23, 2013 |
| Last update date |
Oct 21, 2013 |
| 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 |
GPL4133 |
| Series (1) |
| GSE49175 |
Relationship of mammographic density and gene expression: analysis of normal breast tissue surrounding breast cancer |
|
| 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 |
