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Sample GSM3467091 Query DataSets for GSM3467091
Status Public on Feb 16, 2019
Title semen-BTHO-32
Sample type genomic
 
Channel 1
Source name Sample(semen-BTHO-32)
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 0.950571090980701
CHR01FS000002329 1.0451374640952
CHR01FS000003689 0.760063841106579
CHR01FS000005429 0.95439414114514
CHR01FS000006649 1.18945220530529
CHR01FS000008649 1.11713455953533
CHR01FS000009554 0.813165537270087
CHR01FS000011524 1.63190823774765
CHR01FS000012649 1.3207381370826
CHR01FS000013868 1.2329850324767
CHR01FS000014863 1.24123792406201
CHR01FS000016047 1.02695814135869
CHR01FS000018442 0.978458049886621
CHR01FS000019628 1.12068211630958
CHR01FS000020533 1.2428365447634
CHR01FS000021793 1.18465608465608
CHR01FS000022946 1.15521185597772
CHR01FS000024207 1.10398888668387
CHR01FS000025183 0.991047448522829
CHR01FS000026363 1.49402173913043

Total number of rows: 2066074

Table truncated, full table size 68709 Kbytes.




Supplementary file Size Download File type/resource
GSM3467091_nimblegen_BTHO32_cy3_rawacgh.pair.gz 38.7 Mb (ftp)(http) PAIR
GSM3467091_nimblegen_BTHO32_cy5_rawacgh.pair.gz 38.6 Mb (ftp)(http) PAIR
Processed data included within Sample table

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