|
| Status |
Public on Jul 28, 2015 |
| Title |
1-003C |
| Sample type |
genomic |
| |
|
| Source name |
Saliva
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Saliva
gender: Male
patient relationship: proband
disease state: Cerebral Palsy
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Oragene saliva kits were heated o/n (5pm - 9am) at 50C in an air oven. OG500 saliva kits collected from adults were extracted using Puregene chemistry on an AutopureLS automated DNA extractor. Saliva lysates were RNase a treated prior to extracting using either a 5.0ml or 2.5ml lysate protocol depending on collected saliva volume. OG575 saliva kits collected from children were extracted manually using same Puregene chemistry and RNase A treatment. Pelleted DNA was rehydrated in TE overnight and quantitated next day using Hoescht dye and FLX800 Flurometer.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (LCG-MSM) and primer/neutralization mix (LCG-RPM). After incubation the amplified DNA was fragmented with fragmentation mix (LCG-FMS), precipitated with isopropanol and precipitation mix (LCG-PM1) and resuspended in hybridization buffer (RA1).
|
| |
|
| Hybridization protocol |
RA1 resuspended DNA was loaded onto LCG BeadChip arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
|
| Scan protocol |
After allele-specific staining LCG BeadChip arrays were coated with XC4/ethanol, dried for 10-15 minutes in a flow hood and scanned on an iScan Reader (Illumina).
|
| Data processing |
Genomic DNA extracted from saliva was genotyped using the Illumina HumanOmni2.5M-8v1-1_B. The processed data file "matrix_processed.txt" (available on the series record) contains the GC score, theta, R, B allele frequency, and log R ratios.
|
| |
|
| Submission date |
Jun 30, 2015 |
| Last update date |
Jul 28, 2015 |
| Contact name |
Matthew Gazzellone |
| E-mail(s) |
[email protected]
|
| Phone |
416-813-7032
|
| Organization name |
The Centre for Applied Genomics
|
| Street address |
686 Bay Street
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20641 |
| Series (1) |
| GSE70374 |
Clinically Relevant Copy Number Variations Detected in Cerebral Palsy |
|
