|
| Status |
Public on Mar 19, 2009 |
| Title |
Nimblegen 385K pig array CGH (sample 11, replicate 1) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Boar M, replicate 1
|
| Organism |
Sus scrofa |
| Characteristics |
Genomic DNA from blood of a male Duroc pig, here called boar M
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from lung/liver tissue by the use of Genomic-tip 100/G. Genomic DNA Buffer Set and Genomic DNA Handbook from Qiagen. The precipitation was performed by adding 2.3xvolumes of cold 96% ethanol and 0.1xvolumes of 3M sodium acetate (pH 4.8). After 20 minutes of centrifugation at 4ºC and 13.000 rpm, the precipitated DNA was washed with 70% ethanol, re-precipitated by 5 minutes of centrifugation at 4ºC and 13.000 rpm and resuspended in 1xTE-buffer to a concentration of ~250 ng/μL. After precipitation, the isolated DNA was
resuspended in 1xTE-buffer to a concentration of ~ 250 ng/μL. After precipitation, the isolated DNA was resuspended in 1 mL of 1xTE-buffer (10 mM Tris-HCl, 1 mM EDTA; pH 8).
|
| Label |
Cy3
|
| Label protocol |
DNA labelling was implemented according to the manufacturer’s protocol. Briefly, the DNA was labeled with Cy3 labeled 9mer primers.
|
| |
|
| Channel 2 |
| Source name |
Reference boar R
|
| Organism |
Sus scrofa |
| Characteristics |
Genomic DNA from lung/liver tissue of a male Hampshire pig, here called boar R
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from lung/liver tissue by the use of Genomic-tip 100/G. Genomic DNA Buffer Set and Genomic DNA Handbook from Qiagen. The precipitation was performed by adding 2.3xvolumes of cold 96% ethanol and 0.1xvolumes of 3M sodium acetate (pH 4.8). After 20 minutes of centrifugation at 4ºC and 13.000 rpm, the precipitated DNA was washed with 70% ethanol, re-precipitated by 5 minutes of centrifugation at 4ºC and 13.000 rpm and resuspended in 1xTE-buffer to a concentration of ~250 ng/μL. After precipitation, the isolated DNA was
resuspended in 1xTE-buffer to a concentration of ~ 250 ng/μL. After precipitation, the isolated DNA was resuspended in 1 mL of 1xTE-buffer (10 mM Tris-HCl, 1 mM EDTA; pH 8).
|
| Label |
Cy5
|
| Label protocol |
DNA labelling was implemented according to the manufacturer’s protocol. Briefly, the DNA was labeled with Cy5 labeled 9mer primers.
|
| |
|
| |
| Hybridization protocol |
DNA hybridization was implemented according to the manufacturer’s protocol. Briefly, after the fragmenting by sonification and labelling the test boar A was hybridized against the reference R with a MAUI hybridization system (BioMicro Systems).
|
| Scan protocol |
Scanning and intensity feature extraction were implemented according to the manufacturer’s protocol. Briefly, the array was scanned at 5-micrometer resolution using the GenePix4000B scanner (Axon Instruments, Molecular Devices Corp., Sunnyvale, CA). Data was extracted from scanned images using NimbleScan 2.0 extraction software (NimbleGen Systems, Inc.), which allows for automated grid
alignment, extraction, and generation of data files.
|
| Description |
Detailed descriptions of the above protocols are available in the manufacter´s website.
|
| Data processing |
Loess Normalization with the default parameters (except 'iterations'=10) as implemented in the Limma bioconductor package.
|
| |
|
| Submission date |
Mar 06, 2008 |
| Last update date |
Nov 30, 2017 |
| Contact name |
Jakob Hedegaard |
| E-mail(s) |
Jakob.Hedegaard@ki.au.dk
|
| Phone |
(+45)89991363
|
| Organization name |
Aarhus University, Faculty of Agricultural Sciences
|
| Department |
Department of Genetics and Biotechnology
|
| Lab |
Molecular Genetics and System Biology
|
| Street address |
PO-box 50
|
| City |
Tjele |
| ZIP/Postal code |
DK-8830 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL6553 |
| Series (1) |
| GSE10753 |
A Snapshot of Copy Number Variation in the pig genome |
|
