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Sample GSM1308287 Query DataSets for GSM1308287
Status Public on May 14, 2015
Title Wenchang (WC)
Sample type genomic
 
Channel 1
Source name Blood
Organism Gallus gallus
Characteristics tissue: blood
breed: Wenchang (WC)
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 -0.257243078203
NW_003764381_1FS000005107 0.844565083182
NW_003764381_1FS000005907 0.722326604479
NW_003764381_1FS000006957 1.35653827357
NW_003764381_1FS000007832 -2.01769245833
NW_003764387_1FS000000801 -0.845417711065
NW_003764388_1FS000009412 -0.0873956682332
NW_003764431_1FS000008556 -1.17292823189
NW_003764433_1FS000003851 1.6921364501
NW_003764433_1FS000006841 0.950724345106
NW_003764433_1FS000010891 0.0835065102895
NW_003764435_1FS000007501 0.0723714882669
NW_003764435_1FS000008151 0.808123122073
NW_003764435_1FS000008801 0.187854064348
NW_003764435_1FS000009501 0.180987631259
NW_003764451_1FS000015286 0.379021659427
NW_003764451_1FS000015936 0.776845688805
NW_003764451_1FS000016686 0.605195141028
NW_003764451_1FS000017386 -0.490525869888
NW_003764451_1FS000018036 0.418289472524

Total number of rows: 1387102

Table truncated, full table size 43427 Kbytes.




Supplementary file Size Download File type/resource
GSM1308287_WC_79A01_532.pair.gz 29.3 Mb (ftp)(http) PAIR
GSM1308287_WC_79A01_635.pair.gz 29.2 Mb (ftp)(http) PAIR
Processed data included within Sample table
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