|
| Status |
Public on Mar 17, 2017 |
| Title |
NA12878 Genomic DNA Replicate 1 (IlluminaCytoSNP850K) |
| Sample type |
genomic |
| |
|
| Source name |
Blood, B Lymphocyte
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
ethnicity: Caucasian
cell line: GM12878
|
| Biomaterial provider |
Coriell Cell Repositories https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from GM12878 cell lines by Coriell Cell Repositories
|
| Label |
Cy5, Cy3
|
| Label protocol |
Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html
|
| |
|
| Hybridization protocol |
Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html
|
| Scan protocol |
Performed by manufacturer according to manufacturer's protocol. See protocol at https://support.illumina.com/array/kits.html
|
| Description |
Genomic DNA extracted from GM12878 cell lines. Genomic DNA obtained from Coriell
|
| Data processing |
Raw data in the form of .idat files from the hybridization of NA12878 genomic DNA to the Illumina Infinium human CytoSNP-850K array were obtained from Illumina Inc. The .idat files were processed using the Genotyping Module of the GenomeStudio 2011.1 software package (Illumina Inc., San Diego CA 92122, U.S.A.) with default settings according to the manufacturer's user guide. The required manifest and cluster files were downloaded from http://support.illumina.com/array/downloads.html. Processed data were generated in GenomeStudio in the form of final reports with the required format for downstream CNV analysis using the Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.). Subsequently, CNVs were called using the SNP-FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
The final CNV calls are in the supplementary material of the manuscript.
Processed data are final reports exported from GenomeStudio in the required format for downstream analysis in Nexus Copy Number. Columns include Sample Name (blank field - sample is NA12878), Sample ID (corresponding array barcode and sub-field on which sample was hybridized), SNP Name (equivalent to ID REF - unique identifier for each probe on the array), Chr (chromosome containing probe), Position (chromosomal coordinate of probe), Log R Ratio (the base-2 log of the normalized R value over the expected R value for the theta value (interpolated from the R-values of the cluster)), B Allele Freq (B allele theta value of this SNP for the sample, relative to the cluster positions), GC Score (value between 0 and 1 indicating reliability of genotype call), SNP (Nucleotide substitution for the SNP on the Illumina top strand)
|
| |
|
| Submission date |
Mar 16, 2017 |
| Last update date |
Mar 22, 2017 |
| Contact name |
Rajini Haraksingh |
| E-mail(s) |
rharaksingh@gmail.com
|
| Phone |
2035358367
|
| Organization name |
The University of the West Indies
|
| Department |
Life Sciences
|
| Street address |
The University of the West Indies
|
| City |
St. Augustine |
| ZIP/Postal code |
- |
| Country |
Trinidad and Tobago |
| |
|
| Platform ID |
GPL19718 |
| Series (2) |
| GSE96723 |
Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaCytoSNP850K] |
| GSE96909 |
Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans |
|
