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Sample GSM1085348 Query DataSets for GSM1085348
Status Public on Feb 11, 2016
Title lineA-pool2_RJF
Sample type genomic
 
Channel 1
Source name whole blood
Organism Gallus gallus
Characteristics strain: Line A
tissue: whole blood
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from whole blood using the Wizard Genomic DNA extraction kit per the manufacturers protocol.
Label Cy5
Label protocol The Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol for enzymatic labeling from Agilent Technologies was followed for labeling.
 
Channel 2
Source name whole blood
Organism Gallus gallus
Characteristics strain: Red Jungle Fowl
tissue: whole blood
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from whole blood using the Wizard Genomic DNA extraction kit per the manufacturers protocol.
Label Cy3
Label protocol The Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol for enzymatic labeling from Agilent Technologies was followed for labeling.
 
 
Hybridization protocol The Oligonucleotide Array-Based CGH for Genomic DNA Analysis Protocol for enzymatic labeling from Agilent Technologies was followed for hybridization.
Scan protocol Either an Agilent G2505B Scanner was used following the manufacturers protocol or a GenePix 4100A scanner was used with settings of 5 µm resolution, a saturation tolerance of 0.005% and PMT adjusted to a ratio of 1 ± 0.05
Description Biological replicate 1 of 6 for line A compared to Red Jungle Fowl reference
Data processing Feature extraction was performed using either the Agilent Feature Extraction Software or the GenePix software. Images were processed using R-Bioconductor, Agilent Genomic Workbench version 5.0, and Nexus Copy Number software version 6.1. In R-Bioconductor, data was log2-transformed and normalized by Scale and Centering. Log2 ratios were calculated using each sample as the tester to the red jungle fowl as the reference. This normalized data was processed by the two softwares per the company protocols.
 
Submission date Feb 20, 2013
Last update date Feb 11, 2016
Contact name Jason Abernathy
Organization name USDA-ARS
Lab Aquatic Animal Health Research Unit
Street address 990 Wire Road
City Auburn
State/province AL
ZIP/Postal code 36832
Country USA
 
Platform ID GPL11041
Series (1)
GSE44440 244K array Comparative Genomic Hybridization for the characterization of CNVs among inbred Fayoumi, inbred Leghorn, Line A broiler, and Line B broiler chicken

Data table header descriptions
ID_REF
VALUE Scale and Centering Normalized log2 ratios (test/reference)

Data table
ID_REF VALUE
4 -0.47275
5 -0.1708237
6 -0.2038993
7 0.102356
8 -0.35134452
9 -0.0537525
10 -0.3911686
11 -0.6337616
12 -0.5391071
13 -0.3865888
14 -0.6342224
15 -0.30996431
16 -0.1650707
17 -0.2945518
18 -0.090633
19 -0.2936226
20 0.2523465
21 -0.4373601
22 -0.00824
23 -0.122347

Total number of rows: 237760

Table truncated, full table size 3950 Kbytes.




Supplementary file Size Download File type/resource
GSM1085348_RJF_RJF_Cy3.txt.gz 51.0 Mb (ftp)(http) TXT
GSM1085348_slide1_Cy5.txt.gz 25.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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