|
| Status |
Public on Mar 01, 2011 |
| Title |
Agilent-2087 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Normal whole-spleen tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
tissue: Spleen
|
| Biomaterial provider |
UNC Chapel Hill
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mouse DNA was isolated from either small tissue pellets (20-30 ug) or ethanol precipitated RNA flow through solution. Pellet digestion and DNA isolation steps were in accord with the DNAeasy Mini Kit protocol.
|
| Label |
Cy3
|
| Label protocol |
0.9 ug of genomic DNA digested with Alu I and Rsa I restriction enzymes at 37 degrees Celsius for 2 hours. The reaction was stopped by heating the mixture to 65 degrees Celsius for 20 minutes. Each fragment was then randomly primed at 95 degrees celsius for 3 minutes. Cy3 and Cy5 modified nucleotides were then incorporated by the Large Fragment of DNA Polymerase I (exo klenow fragment) at 37 degrees Celsius for 2 hours.
|
| |
|
| Channel 2 |
| Source name |
Mammary tumor tissue: Mixed_Rb_1.oct22.07_CGH_UHNC_repeat
|
| Organism |
Mus musculus |
| Characteristics |
strain: Mixed
mouse class: Rb1
|
| Biomaterial provider |
UNC Chapel Hill
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mouse DNA was isolated from either small tissue pellets (20-30 ug) or ethanol precipitated RNA flow through solution. Pellet digestion and DNA isolation steps were in accord with the DNAeasy Mini Kit protocol.
|
| Label |
Cy5
|
| Label protocol |
0.9 ug of genomic DNA digested with Alu I and Rsa I restriction enzymes at 37 degrees Celsius for 2 hours. The reaction was stopped by heating the mixture to 65 degrees Celsius for 20 minutes. Each fragment was then randomly primed at 95 degrees celsius for 3 minutes. Cy3 and Cy5 modified nucleotides were then incorporated by the Large Fragment of DNA Polymerase I (exo klenow fragment) at 37 degrees Celsius for 2 hours.
|
| |
|
| |
| Hybridization protocol |
Appropriate cyanine 5- and cyanine 3-labeled DNA sample pairs were combined and then mixed with mouse Cot-1 DNA, Agilent 10X aCGH Blocking Agent, and Agilent 2X Hi-RPM Hybridization Buffer. The labeled target solution was hybridized to Agilent's 244a Mouse Genome CGH microarray (G4415A) using SureHyb chambers. After hybridization the microarrays were washed and dried according to the procedures described in Agilent's protocol.
|
| Scan protocol |
Each microarray slide was scanned at a resolution of 5 um on Agilent G2539A scanner under Scan Control software version A.8.1.3. Spot intensity values were obtained using Agilent aCGH version 4.1 -FE 10 Default Protocol under Agilent Feature Extraction software version 10.1.
|
| Description |
matches to expression sample: Mixed_Rb_1.Oct22.07_UHNC
|
| Data processing |
Data for both channels were Lowess-normalized and then log(2) ratio was taken
|
| |
|
| Submission date |
Feb 24, 2009 |
| Last update date |
Jul 17, 2015 |
| 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 |
GPL4092 |
| Series (1) |
| GSE14457 |
Rb deletion in mammary stem/progenitor epithelium induces tumors with features of luminal-B or basal-like breast cancer |
|
| Data table header descriptions |
| ID_REF |
Spot Reference ID |
| LOG_RAT2N_MEAN |
log2_ratio of channel 2 normalized over channel 1 |
| 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 |
| VALUE |
same as UNF_VALUE but with flagged values removed |
| 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 |
