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Sample GSM1308282 Query DataSets for GSM1308282
Status Public on May 14, 2015
Title Dongxiang (DX)
Sample type genomic
 
Channel 1
Source name Blood
Organism Gallus gallus
Characteristics tissue: blood
breed: Dongxiang (DX)
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 -1.27294980782
NW_003764381_1FS000005107 0.211911783499
NW_003764381_1FS000005907 0.0895788514077
NW_003764381_1FS000006957 1.20259832744
NW_003764381_1FS000007832 -2.41412214521
NW_003764387_1FS000000801 2.77831995167
NW_003764388_1FS000009412 -1.72844732132
NW_003764431_1FS000008556 0.413873859711
NW_003764433_1FS000003851 1.44873557193
NW_003764433_1FS000006841 0.276867074038
NW_003764433_1FS000010891 -0.754292228141
NW_003764435_1FS000007501 1.02524101983
NW_003764435_1FS000008151 -0.672194696958
NW_003764435_1FS000008801 -0.802795600278
NW_003764435_1FS000009501 0.640025958235
NW_003764451_1FS000015286 -0.461171414612
NW_003764451_1FS000015936 0.0448203408593
NW_003764451_1FS000016686 0.154031944364
NW_003764451_1FS000017386 -1.2886350226
NW_003764451_1FS000018036 -0.20680803338

Total number of rows: 1387102

Table truncated, full table size 44382 Kbytes.




Supplementary file Size Download File type/resource
GSM1308282_DX_79A03_532.pair.gz 29.3 Mb (ftp)(http) PAIR
GSM1308282_DX_79A03_635.pair.gz 29.3 Mb (ftp)(http) PAIR
Processed data included within Sample table
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