|
| Status |
Public on Dec 01, 2009 |
| Title |
MCL Agilent 244K aCGH 03-14255 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
03-14255
|
| Organism |
Homo sapiens |
| Characteristics |
MCL Lymph node Biopsy
Lymph node tissue, 57yo male, classic MCL
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard proteinaseK/RNAse followed by Phenol/Chlorofom extraction
|
| Label |
Cy5
|
| Label protocol |
0.5ug of DNA was labelled using standard agilent protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx (
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010)
|
| |
|
| Channel 2 |
| Source name |
Promega Human Male DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Normal Male DNA Promega
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA provided by Promega Part Number G1471
|
| Label |
Cy3
|
| Label protocol |
0.5ug of DNA was labelled using standard agilent protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx (
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010
|
| |
|
| |
| Hybridization protocol |
Standard Agilent Protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx
Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Version 4.0. Part number is G4410-90010.
|
| Scan protocol |
Agilent DNA Microarray Scanner p/n G2565BA.
Scan Region: 61x21.6 mm
Scan Resolution 5 micron
Dye Channel Red & Green
Red and Green PMT 100%
|
| Description |
none
|
| Data processing |
Value represent LOG10 Ratio (CH1/CH2) generated by Standard Agilent Protocols from http://www.opengenomics.com/oligoaCGHLiterature.aspx
Feature extraction protocol CGH-v4_91 was used.
|
| |
|
| Submission date |
Oct 23, 2008 |
| Last update date |
Sep 30, 2009 |
| Contact name |
Ronald J deLeeuw |
| E-mail(s) |
[email protected]
|
| Phone |
6046758111
|
| Fax |
6046758232
|
| Organization name |
BC Cancer Research Centre
|
| Department |
Cancer Genetics
|
| Lab |
Lam Lab
|
| Street address |
675 W. 10th Ave.
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V5Z 1L3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL4544 |
| Series (1) |
| GSE13331 |
Prognostic analysis of mantle cell lymphoma genomes |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Channel 1 (red) / Channel 2 (green) LOG10 Ratio |
| CH2_SIG_MEAN |
Channel 2 (green) Foreground Mean Signal |
| CH1_SIG_MEAN |
Channel 1 (red) Foreground Mean Signal |
| CH2_BKD_MEAN |
Channel 2 (green) Background Mean Signal |
| CH1_BKD_MEAN |
Channel 1 (red) Background Mean Signal |
| CH2_SATURATION |
Channel 2 (green) Saturation |
| CH1_SATURATION |
Channel 1 (red) Saturation |
| CH2_NONUNIFORM |
Channel 2 (green) Spot Non-Uniformity |
| CH1_NONUNIFORM |
Channel 1 (red) Spot Non-Uniformity |
