|
| Status |
Public on Mar 21, 2017 |
| Title |
NA12878 Genomic DNA Replicate 2 (IlluminaHumanCoreExome) |
| Sample type |
genomic |
| |
|
| Source name |
Blood, B Lymphocyte
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
ethnicity: Caucasian
cell line: GM12878
|
| Biomaterial provider |
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA12878
|
| 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 HumanCoreExome v1.1 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.
|
| |
|
| Submission date |
Mar 20, 2017 |
| Last update date |
Mar 21, 2017 |
| Contact name |
Rajini Haraksingh |
| E-mail(s) |
[email protected]
|
| 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 |
GPL23195 |
| Series (2) |
| GSE96816 |
Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaHumanCoreExome] |
| GSE96909 |
Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans |
|
