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Sample GSM3467085 Query DataSets for GSM3467085
Status Public on Feb 16, 2019
Title semen-BTHO-26
Sample type genomic
 
Channel 1
Source name Sample(semen-BTHO-26)
Organism Bos taurus
Characteristics tissue: semen
gender: male
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from semen or blood using a Qiagen DNEasy tissue and blood kit (QIAGEN, Valencia, CA, USA).
Label Cy3
Label protocol Labeling was performed by the third party provider, Nimblegen
 
Channel 2
Source name Reference (L1 Dominette whole blood DNA extract)
Organism Bos taurus
Characteristics tissue: Blood
gender: female
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from semen or blood using a Qiagen DNEasy tissue and blood kit (QIAGEN, Valencia, CA, USA).
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 pair file coordinates for probe locations. The initial data analysis (normalization and segmentation) was performed on NimbleScan v2.6 software with segMNT algorithm. log2-transformed (test/control) ratios.
Data processing Processed data files are pair file coordinates for probe locations. The initial data analysis (normalization and segmentation) was performed on NimbleScan v2.6 software with segMNT algorithm.
 
Submission date Nov 13, 2018
Last update date Feb 16, 2019
Contact name George E Liu
E-mail(s) [email protected]
Phone 13015049843
Organization name USDA
Street address 10300 Baltimore Avenue
City Beltsville
ZIP/Postal code 207705
Country USA
 
Platform ID GPL11314
Series (1)
GSE122478 Genome-Wide Detection of CNVs and Their Association with Complex Traits in Holsteins

Data table header descriptions
ID_REF
VALUE NimbleScan 2.6 software computed, log2-transformed (test/control) ratios

Data table
ID_REF VALUE
CHR01FS000001168 0.841372396123427
CHR01FS000002329 1.07902634211404
CHR01FS000003689 1.14227434982152
CHR01FS000005429 0.897832817337461
CHR01FS000006649 1.26146462851049
CHR01FS000008649 1.26363125351321
CHR01FS000009554 0.804890219560878
CHR01FS000011524 1.52657004830918
CHR01FS000012649 1.14452423698384
CHR01FS000013868 1.24538352272727
CHR01FS000014863 0.965509770787296
CHR01FS000016047 1.05570117955439
CHR01FS000018442 1.22528850978424
CHR01FS000019628 1.26931953283446
CHR01FS000020533 1.22152403282532
CHR01FS000021793 1.04371751757872
CHR01FS000022946 1.16164921465969
CHR01FS000024207 1.23710664335664
CHR01FS000025183 0.960552268244576
CHR01FS000026363 1.32220943613349

Total number of rows: 2066074

Table truncated, full table size 68658 Kbytes.




Supplementary file Size Download File type/resource
GSM3467085_nimblegen_BTHO26_cy3_rawacgh.pair.gz 38.6 Mb (ftp)(http) PAIR
GSM3467085_nimblegen_BTHO26_cy5_rawacgh.pair.gz 38.6 Mb (ftp)(http) PAIR
Processed data included within Sample table

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