NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2544623 Query DataSets for GSM2544623
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) 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 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

Supplementary file Size Download File type/resource
GSM2544623_9374344161_R02C01_Grn.idat.gz 3.9 Mb (ftp)(http) IDAT
GSM2544623_9374344161_R02C01_Red.idat.gz 3.7 Mb (ftp)(http) IDAT
GSM2544623_HumanCoreExome-12v1-1_NexusFinalReport2.txt.gz 8.8 Mb (ftp)(http) TXT
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap