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Sample GSM1308286 Query DataSets for GSM1308286
Status Public on May 14, 2015
Title Tibetan (TB)
Sample type genomic
 
Channel 1
Source name Blood
Organism Gallus gallus
Characteristics tissue: blood
breed: Tibetan (TB)
gender: Female
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated using standard phenol/chloroform extraction methods.
Label Cy3
Label protocol 0.5 ug of test DNA were labeled with Cy3 and 0.5 ug of reference DNA were labeled with Cy5 following NimbleGen Arrays User's Guide.
 
Channel 2
Source name Blood
Organism Gallus gallus
Characteristics tissue: blood
breed: Red Jungle Fowl
gender: Female
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated using standard phenol/chloroform extraction methods.
Label Cy5
Label protocol 0.5 ug of test DNA were labeled with Cy3 and 0.5 ug of reference DNA were labeled with Cy5 following NimbleGen Arrays User's Guide.
 
 
Hybridization protocol Hybridization was done for 40-72 h on 42℃ using NibleGen Hybridization System, and all the washing and drying steps were done without interruption.
Scan protocol NimbleGem arrays were scanned at 2 μm resolution using a NimbleGem MS200 scanner with PMT 100%
Data processing NimbleScan Software Version 2.6 (Roche NimbleGen, Inc) was used to extract the data. Considering we only analyzed raw CGH log2 ratio values not processed/normalized data, log2 ratio values were calculated between tests and reference.
 
Submission date Jan 15, 2014
Last update date May 14, 2015
Contact name Guoqiang Yi
E-mail(s) yiguoqiang20@hotmail.com
Phone +8662731351
Organization name Agricultural Genome Institute at Shenzhen
Street address No 7,Pengfei Road,Dapeng District,Shenzhen
City Shenzhen
State/province Guangdong
ZIP/Postal code 518120
Country China
 
Platform ID GPL18174
Series (2)
GSE54117 Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 1)
GSE54119 Validation experiment of copy number variations identified by next-generation sequencing in chickens

Data table header descriptions
ID_REF
VALUE log2 ratio Cy3/Cy5

Data table
ID_REF VALUE
NW_003764381_1FS000003506 0.282536490389
NW_003764381_1FS000005107 -0.177300784728
NW_003764381_1FS000005907 -0.0989119366575
NW_003764381_1FS000006957 0.575481799717
NW_003764381_1FS000007832 -0.567241637636
NW_003764387_1FS000000801 -0.868477021357
NW_003764388_1FS000009412 -1.32701351363
NW_003764431_1FS000008556 -1.77513091963
NW_003764433_1FS000003851 0.592255816927
NW_003764433_1FS000006841 -0.550009342147
NW_003764433_1FS000010891 -0.386020565302
NW_003764435_1FS000007501 -1.25566651081
NW_003764435_1FS000008151 -0.181747287123
NW_003764435_1FS000008801 -0.790594956788
NW_003764435_1FS000009501 0.258054183423
NW_003764451_1FS000015286 -0.615159874577
NW_003764451_1FS000015936 -0.187955643392
NW_003764451_1FS000016686 -0.210070764038
NW_003764451_1FS000017386 -1.07467543796
NW_003764451_1FS000018036 -0.583787472644

Total number of rows: 1387102

Table truncated, full table size 44430 Kbytes.




Supplementary file Size Download File type/resource
GSM1308286_TB_79A02_532.pair.gz 29.2 Mb (ftp)(http) PAIR
GSM1308286_TB_79A02_635.pair.gz 29.2 Mb (ftp)(http) PAIR
Processed data included within Sample table
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