|
| Status |
Public on Jan 31, 2021 |
| Title |
MMTV_ErbB2_Project-0131_4-T5_Grubbs |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Whole Mouse Reference RNA-2009
|
| Organism |
Mus musculus |
| Characteristics |
reference: Whole Mouse Reference
|
| Biomaterial provider |
produced at UNC
|
| Treatment protocol |
described in He et al., 2004. BioTechniques, Vol. 37:464-468
|
| Growth protocol |
described in He et al., 2004. BioTechniques, Vol. 37:464-468
|
| 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 |
DMBA treated MMTV-Neu+/- tumor RNA
|
| Organism |
Mus musculus |
| Characteristics |
tumor: Mouse tumor derived RNA
genotype/variation: MMTV-Neu+/-
|
| Biomaterial provider |
Clinton Grubbs and Ron Lubet University of Alabama
|
| Treatment protocol |
described in Hu et al., 2005, BioTechniques, 38:121-124
|
| Growth protocol |
described in Hu et al., 2005, BioTechniques, 38:121-124
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA
|
| Label |
Qiagen Rneasy Kit
|
| 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 |
Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software
|
| Description |
DMBA treated MMTV-Neu+/- tumor RNA versus whole mouse reference RNA
|
| Data processing |
Data for both channels were Lowess-normalized and then log(2) ratio was taken
|
| |
|
| Submission date |
Sep 29, 2011 |
| Last update date |
Jan 31, 2021 |
| 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 |
GPL4134 |
| Series (1) |
| GSE35188 |
DIMETHYLBENZANTHRACENE (DMBA) INDUCED MAMMARY CARCINOGENESIS IN MMTV-Neu and MMTV/p53 KO FEMALE MICE AND EFFECTS OF REXINOIDS |
|
| 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 |
