|
| Status |
Public on Jan 07, 2014 |
| Title |
538.02P |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Total DNA from sample 538.02P labeled with Cyanine-5 (red).
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Amniotic Fluid
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAamp DNA Mini Kit
|
| Label |
Cy5
|
| Label protocol |
Between 300 and 400ng of total genomic DNA were labeled using Cy5-modified dCTP by random priming method, according to a slightly modified Bioprime Kit protocol (Invitrogen). Absorbance measures at 532 and 650nm. determined the amounts of dye incorporated to the DNA.
|
| |
|
| Channel 2 |
| Source name |
Total DNA from reference sample 20M labeled with Cyanine-3 (green).
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: fresh peripheral blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chemagen magnetic beads. Chemagic DNA Blood Kit special (cat. num 703, Chemagen)
|
| Label |
Cy3
|
| Label protocol |
Between 300 and 400ng of total genomic DNA were labeled using Cy3-modified dCTP by random priming method, according to a slightly modified Bioprime Kit protocol (Invitrogen). Absorbance measures at 532 and 650nm. after removing unincorporated dye determined the amount of dye incorporation.
|
| |
|
| |
| Hybridization protocol |
Hybridisation was performed as described in Wang. NJ. et al, Am. J. Hum. Genet, 75(2), 267-81, 2004.
|
| Scan protocol |
Agilent Microarray Scanner (G2565CA - Agilent Inc., Palo Alto, CA). Images were extracted with Genepix Pro 6.0 (Axon, Inc) using the irregular spot finding features with default flagging settings.
|
| Description |
biological sample used as control/testing purposes in the study.
|
| Data processing |
In order to extract information from the GenePix generated files, we used an in-house developed pipeline called Bacanal (Lozano et al, unpublished). For lowess normalization of spot signals it relies on a bioconductor package called LIMMA. Values provided correspond to the log2 Cy5/Cy3 (test/reference) ratios.
|
| |
|
| Submission date |
Jan 12, 2011 |
| Last update date |
Jan 07, 2014 |
| Contact name |
Lluis Armengol |
| Organization name |
qGenomics
|
| Street address |
Doctor Aiguader, 88
|
| City |
BARCELONA |
| State/province |
Catalonia |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11395 |
| Series (1) |
| GSE26654 |
use of aCGH in a large series of prenatal samples |
|
