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Sample GSM2544975 Query DataSets for GSM2544975
Status Public on Mar 22, 2017
Title NA12878 Genomic DNA Replicate 1 (HumanOmni2.5Exome)
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 HumanOmni2.5Exome 8v1 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 21, 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 GPL23200
Series (2)
GSE96846 Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaHumanOmni2.5Exome]
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
GSM2544975_9464957012_R02C01_Grn.idat.gz 17.3 Mb (ftp)(http) IDAT
GSM2544975_9464957012_R02C01_Red.idat.gz 17.4 Mb (ftp)(http) IDAT
GSM2544975_HumanOmni25Exome-8v1_NexusFinalReport1.txt.gz 42.9 Mb (ftp)(http) TXT
Processed data provided as supplementary file

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