|
| Status |
Public on Jul 13, 2015 |
| Title |
Case 6463 poc child cyto12b 6159151127_R04C02 |
| Sample type |
genomic |
| |
|
| Source name |
Case 6463 poc child cyto12b 6159151127_R04C02
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: 6159151127_R04C02
case id: 6463
sample type: poc
tissue: products of conception
subject: child
array type: cyto12b
|
| Treatment protocol |
Visual examination of the sample to determine if villi is present. Separation of villi from maternal tissue performed using scalple. Refrigeration if sample is not processed immediately
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen Dneasy
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
Unique barcodes are affixed to the sample and associated within an internal sample tracking system
|
| |
|
| Hybridization protocol |
Illumunian infinium process
|
| Scan protocol |
Illumunian infinium process using iScan
|
| Data processing |
All the raw data comes from illumina arrays. Illumina also post-processes the data using Bead Studio to create the b-allele-frequency number and log-r-ratio. We use the b-allele-frequency in our analysis.
In some cases the post processing does not provide the b-allele-frequency numbers. In those cases, we calculate radial and theta numbers for each snip. The formulas are radial = sqrt(chX^2+chY^2) theta = arcsine(chY/radial) This is done on per snip bases where chX and chY are the raw counts. If both are 0, the output is not-a-number.
Series supplementary files contain raw X and Y signals only
|
| |
|
| Submission date |
Jul 13, 2012 |
| Last update date |
Jul 13, 2015 |
| Contact name |
Jennifer Dikan |
| E-mail(s) |
[email protected]
|
| Organization name |
Natera
|
| Street address |
201 Industrial Road, Suite 410
|
| City |
San Carlos |
| State/province |
California |
| ZIP/Postal code |
94070 |
| Country |
USA |
| |
|
| Platform ID |
GPL13829 |
| Series (1) |
| GSE39332 |
Chromosomal analysis of products of conception |
|
