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Sample GSM961501 Query DataSets for GSM961501
Status Public on Jul 13, 2015
Title Case 8244 poc child cyto12b 6264365020_R03C01
Sample type genomic
Source name Case 8244 poc child cyto12b 6264365020_R03C01
Organism Homo sapiens
Characteristics sample id: 6264365020_R03C01
case id: 8244
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
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

Supplementary data files not provided
Processed data not provided for this record

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