|
Status |
Public on Jan 07, 2014 |
Title |
ADN434 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Total DNA from sample ADN434 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.
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|
|
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information from the GenePix generated files, we used an in-house developed pipeline called Bacanal (Lozano et al, unpublished).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.
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|
|
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 |
|