|
Status |
Public on Sep 04, 2008 |
Title |
breast cancer patient sample #40387 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
breast cancer patient sample #40387
|
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.
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|
|
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 |
|