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Sample GSM2545800 Query DataSets for GSM2545800
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

Supplementary file Size Download File type/resource
GSM2545800_Agilent4x180K_CGH_NA12878_Replicate1_FE.txt.gz 50.7 Mb (ftp)(http) TXT
GSM2545800_Agilent_4x180K_Replicate_1.txt.gz 6.9 Kb (ftp)(http) TXT
Processed data provided as supplementary file

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