|
| Status |
Public on Jul 30, 2007 |
| Title |
PB407 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs
|
| 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 |
Breast Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
age: 56
er (1=positive; 0=negative): 1
pgr (1=positive; 0=negative): --
her2 clinical status ihc/fish (1=positive; 0=negative): 0
node status (1=positive=1 or more nodes+; 0=negative): 1
grade: 3
size (1= <=2cm; 2= >2cm to <=5cm; 3=>5cm; 4=any size with direct extension to chest wall or skin): 3
rfs event (0=no relapse, 1=relapsed at any site or died of disease): 1
rfs months: 9
overall survival event (0=alive, 1=dod or doc): 0
overall suvival months: 17
pam50 predictions plus claudin-low classification (cell line predictor): LumB
dscores unc337: 0.041379815
|
| 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 4.1 analysis software.
|
| Description |
Age: 56, ER status: positive, Node status: positive, grade: 3, Size: larger than 5cm, RFS event: relapsed or died of disease, RFS months: 9, Overall survival event: alive, Overall survival months: 17, Single Sample Predictor Subtype: LuminalB
|
| Data processing |
Data for both channels were Lowess-normalized and then log(2) ratio was taken
|
| |
|
| Submission date |
Jun 02, 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 |
GPL887 |
| Series (7)
|
| GSE2740 |
Estrogen-regulated genes predict survival in estrogen receptor and/or progesterone receptor-positive breast cancers |
| GSE3165 |
Identification of conserved gene expression features across human and murine mammary tumors |
| GSE3521 |
A compact VEGF signature associated with distant metastases and poor outcomes |
| GSE6130 |
Agreement in Breast Cancer Classification between Microarray and qRT-PCR from Fresh-Frozen and Formalin-Fixed Tissues |
| GSE10885 |
An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. |
| GSE10893 |
Basal-like Breast Cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival |
| GSE18229 |
Phenotypic and Molecular Characterization of the Claudin-low Intrinsic Subtype of 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 |
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