|
Status |
Public on Feb 23, 2005 |
Title |
Sum149-C-2nd-stripped |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
|
Organism |
Homo sapiens |
Extracted molecule |
total RNA |
|
|
Channel 2 |
Source name |
"Breast tumor derived line SUM149 (Ethier et al., Cancer Res, 53: 627-635, 1993)"
|
Organism |
Homo sapiens |
Extracted molecule |
total RNA |
|
|
|
Description |
Breast tumor derived line SUM149 Keywords = Agilent microarray, Stripped arrays, Replicate reproducibility
|
|
|
Submission date |
Aug 25, 2004 |
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 |
GPL887 |
Series (1) |
GSE1706 |
High Reproducibility Using Sodium Hydroxide Stripped Long Oligonucleotide DNA Microarrays |
|
Data table header descriptions |
ID_REF |
|
VALUE |
same as UNF_VALUE but with flagged values removed |
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 (CH2IN_MEAN - CH2BN_MEDIAN) over (CH1_MEAN - CH1_BKD_MEDIAN), CH2IN_MEAN and CH2BN_MEDIAN are global-normalized intensities |
CORR |
correlation coefficient among pixels |
FLAG |
Spot flag. 0:not flagged; negative:flagged as bad spots; positive:flagged as good spots |
CONTROL |
Y: control gene; N: not control |
UNF_VALUE |
LOG_RAT2L_MEAN; log2_ratio of CH2DL_MEAN over CH1DL_MEAN |