|
| Status |
Public on Sep 04, 2008 |
| Title |
breast cancer patient sample #9997 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
breast cancer patient sample #9997
|
| Organism |
Homo sapiens |
| Characteristics |
human breast cancer with basal-like feature
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted using Qiagen Dneasy mini kit following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
10 ng of genomic DNA was amplified with phi29 DNA polymerase at 30°C for 16 hours. Amplified DNA was then digested with 50 units of Alu I and Rsa I at 37° for 2 hours and purified by using QIAQuick PCR clean-up kit. Labeling reactions were performed with 7 ug aliquots of this DNA at 37C for 3 hours using BioPrime Array CGH Genomic Labeling Module with 3 umol Cy5- or Cy3-dUTP, Invitrogen. Labeled samples were purified , concentrated on a Centricon YM-30 column, Millipore.
|
| |
|
| Channel 2 |
| Source name |
human female blood pooled genomic DNA, Promega
|
| Organism |
Homo sapiens |
| Characteristics |
human female pooled genomic DNA, Promega
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted using Qiagen Dneasy mini kit following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
10 ng of genomic DNA was amplified with phi29 DNA polymerase at 30°C for 16 hours. Amplified DNA was then digested with 50 units of Alu I and Rsa I at 37° for 2 hours and purified by using QIAQuick PCR clean-up kit. Labeling reactions were performed with 7 ug aliquots of this DNA at 37C for 3 hours using BioPrime Array CGH Genomic Labeling Module with 3 umol Cy5- or Cy3-dUTP, Invitrogen. Labeled samples were purified , concentrated on a Centricon YM-30 column, Millipore.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
Images were quantified using Agilent Feature Extraction Software (version A.7.5) array CGH data extraction protocol.
|
| Description |
individual patient sample
|
| Data processing |
Linear normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
|
| |
|
| Submission date |
Sep 03, 2008 |
| Last update date |
Sep 08, 2008 |
| Contact name |
Wayne Yu |
| E-mail(s) |
wyu8@jhmi.edu
|
| Phone |
(410)502-7970
|
| Fax |
(410)955-8780
|
| Organization name |
Johns Hopkins University
|
| Department |
Cancer Center
|
| Street address |
417 N. Caroline St.
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL2879 |
| Series (1) |
| GSE12659 |
Chromosomal changes in aggressive breast cancers with basal-like features |
|
