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Sample GSM1537668 Query DataSets for GSM1537668
Status Public on Nov 04, 2015
Title semen-BTJE4
Sample type genomic
 
Channel 1
Source name frozen semen stock
Organism Bos taurus
Characteristics gender: male
breed: Jersey
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from semen using a Qiagen DNEasy tissue and blood kit
Label Cy3
Label protocol Labeling was performed by the third party provider, Nimblegen
 
Channel 2
Source name L1 Dominette whole blood DNA extract
Organism Bos taurus
Characteristics gender: female
breed: Hereford
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from semen using a Qiagen DNEasy tissue and blood kit
Label Cy5
Label protocol Labeling was performed by the third party provider, Nimblegen
 
 
Hybridization protocol Hybridization was performed by the third party provider, Nimblegen. Dye swap experiments with the Dominette reference sample were performed to test probe quality
Scan protocol Scanning was performed by the third party provider, Nimblegen
Description Processed data files are bed file coordinates for probe locations. Columns 4 and 5 indicate the normalized aCGH copy number value and the rCV value, respectively
Data processing Data processing was performed similar to Sudmant et al. 2010 's single channel aCGH methodology. In short, single channel array intensities were transformed into integer copy number estimates by using normalized reference signal intensity derived from all tested array samples.
Median reference signal intensity normalized log2 ratios, and rCV estimates of probe sequence copy number fluctuation.
 
Submission date Nov 05, 2014
Last update date Nov 04, 2015
Contact name Derek Martens Bickhart
E-mail(s) derek.bickhart@ars.usda.gov
Phone 301 504 8592
Organization name USDA ARS
Department BARC
Lab AGIL
Street address Building 005, Rm 318, BARC-West 10300 Baltimore Ave
City Beltsville
State/province MD
ZIP/Postal code 20705
Country USA
 
Platform ID GPL11314
Series (1)
GSE62990 Next generation sequencing reveals the diversity and population-genetic properties of cattle CNVs

Supplementary file Size Download File type/resource
GSM1537668_BTJE4.btf3.umd3.acgh.bed.gz 18.1 Kb (ftp)(http) BED
GSM1537668_nimblegen_BTJE4_cy3_rawacgh.pair.gz 38.7 Mb (ftp)(http) PAIR
GSM1537668_nimblegen_BTJE4_cy5_rawacgh.pair.gz 38.7 Mb (ftp)(http) PAIR
Processed data provided as supplementary file

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