|
| Status |
Public on Mar 23, 2017 |
| Title |
NA12878 Genomic DNA Replicate 1 (Agilent022060) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| 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 and GM10851 cell lines by Coriell Cell Repositories
|
| Label |
cy3
|
| Label protocol |
Performed by manufacturer-recommended service provider according to manufacturer's protocol. See protocol at http://www.genomics.agilent.com/en/SurePrint-CGH-CNV-Microarrays/Human-Genome-CGH-Microarrays/?cid=AG-PT-110&tabId=AG-PR-1079&navAction=pop
|
| |
|
| Channel 2 |
| Source name |
Blood, B Lymphocyte
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
ethnicity: Caucasian
cell line: GM10851
|
| Biomaterial provider |
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA10851
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from GM12878 and GM10851 cell lines by Coriell Cell Repositories
|
| Label |
cy5
|
| Label protocol |
Performed by manufacturer-recommended service provider according to manufacturer's protocol. See protocol at http://www.genomics.agilent.com/en/SurePrint-CGH-CNV-Microarrays/Human-Genome-CGH-Microarrays/?cid=AG-PT-110&tabId=AG-PR-1079&navAction=pop
|
| |
|
| |
| Hybridization protocol |
Performed by manufacturer-recommended service provider according to manufacturer's protocol. See protocol at http://www.genomics.agilent.com/en/SurePrint-CGH-CNV-Microarrays/Human-Genome-CGH-Microarrays/?cid=AG-PT-110&tabId=AG-PR-1079&navAction=pop
|
| Scan protocol |
Performed by manufacturer-recommended service provider according to manufacturer's protocol. See protocol at http://www.genomics.agilent.com/en/SurePrint-CGH-CNV-Microarrays/Human-Genome-CGH-Microarrays/?cid=AG-PT-110&tabId=AG-PR-1079&navAction=pop
|
| Description |
Test sample (ch1) = NA12878, Control sample (ch2) = NA10851
|
| Data processing |
Raw data in the form of Feature Extraction (FE) files from the hybridization of NA12878 and NA10851 genomic DNA to the Agilent SurePrint G3 Human CGH Microarray 4x180K (Design ID 022060) were obtained from Agilent-recommended service providers. The FE files were processed to obtain CNV calls by using both Agilent Genomic Workbench 7.0.4.0 (Agilent Technologies, Santa Clara CA 95051, U.S.A.) and Nexus Copy Number 7.5 software package (BioDiscovery, Hawthorne CA 90250, U.S.A.) software packages. CNV calls were obtained by generating Interval Based Reports using Agilent Genomic Workbench with default settings according to the manufacturer's user guide, and by using the FASST2 Segmentation Algorithm in the Nexus Copy Number software package.
Processed data are interval based reports generated using the ADM-2 algorithm in the Agilent Genomic Workbench software package. Header information lists the specific parameters used for the analysis. Columns include Chr (chromosome of CNV), Cytoband (cytoband of CNV), Start (start coordinate of CNV), Stop (stop coordinate of CNV), #Probes (number of probes in CNV interval), Amplification (Base2 log ratio indicating an amplification in the genome of NA12878 compared to that of NA10851), Deletion (Base2 log ratio indicating a deletion in the genome of NA12878 compared to that of NA10851), pval (p value), Gene Names (names of any genes overalpping with the CNV interval)
There are no intermediate processed files containing values for every probe. The only output generated were the final CNV calls from these software packages.
|
| |
|
| Submission date |
Mar 22, 2017 |
| Last update date |
Mar 23, 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 |
GPL10123 |
| Series (2) |
| GSE96905 |
Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [Agilent022060] |
| GSE96909 |
Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans |
|
