|
| Status |
Public on Feb 20, 2007 |
| Title |
HME-CC+p53RNAi, 24h sham |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
HME-CC pool
|
| Organism |
Homo sapiens |
| Characteristics |
Cell Line messenger RNA
|
| Biomaterial provider |
Melissa Troester UNC-CH
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Harvest cells by scraping, use invitrogen Micro-FastTrack to extract mRNA
|
| Label |
Cy3
|
| Label protocol |
Agilent direct labeling kit
|
| |
|
| Channel 2 |
| Source name |
HME-CC+p53RNAi, 24h sham
|
| Organism |
Homo sapiens |
| Characteristics |
Cell Line messenger RNA
|
| Biomaterial provider |
Melissa Troester UNC-CH
|
| Growth protocol |
Cells grown for to 60-80% confluence in MEGM media (Clonetics), harvested 48 hours after feeding, 4 harvests were pooled
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Harvest cells by scraping, use invitrogen Micro-FastTrack to extract mRNA
|
| Label |
Cy5
|
| Label protocol |
Agilent direct labeling kit
|
| |
|
| |
| Hybridization protocol |
Agilent direct labeling kit
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.1 analysis software
|
| Description |
HME-CC+p53RNAi, 24h sham
|
| Data processing |
Data was filtered for Lowess normalized net (mean) >30 in both channels and flagged values removed, only genes with 70% good data were used, log base 2 expression ratios given in the data table.
|
| |
|
| Submission date |
Aug 23, 2005 |
| Last update date |
Jul 17, 2015 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
[email protected]
|
| 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 |
GPL885 |
| Series (1) |
| GSE3178 |
Gene expression patterns associated with p53 status in breast cancer |
|
| Data table header descriptions |
| ID_REF |
Spot Reference ID |
| 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 |
