|
| Status |
Public on Mar 18, 2011 |
| Title |
M200489 |
| 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 |
Total RNA isolated by stratagene
|
| Label |
Cy3
|
| Label protocol |
described in Hu et al., 2005, BioTechniques, 38:121-124
|
| |
|
| Channel 2 |
| Source name |
M200489
|
| Organism |
Homo sapiens |
| Characteristics |
slidename: H1AUNC44K-H1-0499
sample: M200489
study: Xena
intrinsic subtypes by pam50: LumA
p53 status by amplichip: MUTANT
p53 measured by ihc: POSITIVE
tumor size (cm): 5
grade: 2
er (0 = negative; 1 = positive): 1
pgr (0 = negative; 1 = positive): 0
her2 (0 = negative; 1 = positive): 0
response: PARTIAL RESPONSE
neoadjuvant chemotherapy: docetaxel-Capecitabine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy Kit
|
| Label |
Cy5
|
| 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 |
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 5.1 analysis software.
|
| Description |
M200489
|
| Data processing |
Data for both channels were Lowess-normalized and then log(2) ratio was taken
|
| |
|
| Submission date |
Feb 11, 2010 |
| Last update date |
Jun 06, 2022 |
| 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 |
GPL5325 |
| Series (1) |
| GSE22358 |
Clinical and Pathologic Response of the Primary Tumor in Women Receiving Neoadjuvant Docetaxel-Capecitabine (+/- Trastuzumab) Chemotherapy |
|
| Relations |
| Reanalyzed by |
GSE205568 |
| 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 |
|
| 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 |
| UNF_VALUE |
log2_ratio of CH2DL_MEAN over CH1DL_MEAN (LOG_RAT2L_MEAN) |
