|
| Status |
Public on Jul 20, 2018 |
| Title |
Mixed_Brg1het_T2023_CGH_Bultman |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DNA reference
|
| Organism |
Mus musculus |
| Characteristics |
reference: DNA reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA isolated using Dneasy kit (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
labeled according to the direct incorporation method (Agilent)
|
| |
|
| Channel 2 |
| Source name |
Mixed_Brg1het_T2023_CGH_Bultman
|
| Organism |
Mus musculus |
| Characteristics |
tumor: mammary tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen Dneasy Kit
|
| Label |
Cy5
|
| Label protocol |
labeled according to the direct incorporation method (Agilent)
|
| |
|
| |
| Hybridization protocol |
hybridized to Agilent 244k CGH arrays (model G4415A)
|
| Scan protocol |
scanned on Agilent scanner (model G2505B)
|
| Description |
mammary tumor
|
| Data processing |
Data for both channels were Lowess-normalized and then log(2) ratio was taken
|
| |
|
| Submission date |
Jul 26, 2013 |
| Last update date |
Jul 20, 2018 |
| Contact name |
Charles Perou |
| E-mail(s) |
[email protected]
|
| Phone |
919-843-5740
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
CB#7295
|
| Street address |
102 Mason Farm Road
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7295 |
| Country |
USA |
| |
|
| Platform ID |
GPL4092 |
| Series (1) |
| GSE52173 |
Across-species comprehensive copy number analyses identifies subtype-specific drivers of breast cancer development |
|
| 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 |
