|
| Status |
Public on Mar 29, 2013 |
| Title |
IBC#5 (DNA) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
IBC, core-biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: IBC
her2: 0
er: 0
|
| Treatment protocol |
For tumor samples, 5–20 frozen sections of biopsy (16 μm thick) were manually microdissected. Under the guidance of a pathologist, normal tissue was removed leaving tumor cells comprising greater than 90% of the specimen. For normal breast samples, 40–60 frozen sections of surgical specimen (16 μm thick) were subjected for microdissection manually.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Quick Gene SP-kit DNA tissue (Fujifilm; Tokyo, Japan), and quality was characterized with Agarose gel electrophoresis. Human Female Genomic DNA (Novagen; Madison, WI, USA) was used for normal reference DNA.
|
| Label |
Alexa 555
|
| Label protocol |
Alu I and Rsa I-restricted genomic DNAs were labeled by random priming with Alexa555-dCTP (test DNA) and Alexa647-dCTP (reference DNA) using the BioPrime Plus ArrayCGH Indirect Genomic Labeling System (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
Human Female Genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tag: Novagen Catalogue Number: 70605
|
| Treatment protocol |
For tumor samples, 5–20 frozen sections of biopsy (16 μm thick) were manually microdissected. Under the guidance of a pathologist, normal tissue was removed leaving tumor cells comprising greater than 90% of the specimen. For normal breast samples, 40–60 frozen sections of surgical specimen (16 μm thick) were subjected for microdissection manually.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Quick Gene SP-kit DNA tissue (Fujifilm; Tokyo, Japan), and quality was characterized with Agarose gel electrophoresis. Human Female Genomic DNA (Novagen; Madison, WI, USA) was used for normal reference DNA.
|
| Label |
Alexa 647
|
| Label protocol |
Alu I and Rsa I-restricted genomic DNAs were labeled by random priming with Alexa555-dCTP (test DNA) and Alexa647-dCTP (reference DNA) using the BioPrime Plus ArrayCGH Indirect Genomic Labeling System (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
Labeled test and reference DNAs were ethanol precipitated in the presence of Cot-1 DNA, redissolved in a hybridization mix, and denatured at 70C for 10 min. After incubation at 42C for 5 min, the mixture was applied to Whole Genome DNA Microarray (LinkGenomics) covered with a MAUI Mixer hybridization chamber (Biomicro systems). After incubation at 42C for 48 hours, the slides were then washed with 2xSSC/0.1%SDS buffer and 0.1xSSC/0.1%SDS buffer several times. After rinsing with 0.01xSSC buffer and air-drying.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting (Scan resolution 10um, Dye channel is set to Red/Green and PMT is set to Hi 100%, Lo 10%).
|
| Description |
Data was merged high (_100) and low (_10) PMT data
|
| Data processing |
Extract tif images using the Gene-Pix Pro 4.0 imaging software (Axon Instruments; Union City, CA, USA). High PMT data and Low PMT data were marged. Normalization was performed using global-normalization methods.
|
| |
|
| Submission date |
Mar 28, 2013 |
| Last update date |
Mar 29, 2013 |
| Contact name |
Takahiro Kogawa |
| E-mail(s) |
tkogawa1@mdanderson.org
|
| Organization name |
MD Anderson
|
| Department |
Breast Medical
|
| Street address |
1515 Holcomb Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL16895 |
| Series (2) |
| GSE45582 |
Genomic Analysis of Microdissected Inflammatory Breast Cancer |
| GSE45584 |
Expression Analysis and Genomic Analysis of Microdissected Inflammatory Breast Cancer |
|
