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Sample GSM1085351 Query DataSets for GSM1085351
Status Public on Feb 11, 2016
Title RJF_Leghorn-ind1
Sample type genomic
 
Channel 1
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 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: White Leghorn
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 Red Jungle Fowl reference compared to Biological replicate 1 of 6 for Leghorn
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 0.0315827
5 0.0173276
6 -0.1045292
7 0.249678
8 -0.0154211
9 0.123145156
10 -0.2778038
11 -0.4694673
12 -0.6187423
13 0.1566781
14 -0.3620882
15 -0.0686114
16 0.0280519
17 0.17613255
18 0.2398409
19 -0.2421383
20 -0.0350908
21 -0.0769195
22 0.3539
23 0.628551

Total number of rows: 237760

Table truncated, full table size 3948 Kbytes.




Supplementary file Size Download File type/resource
GSM1085351_RJF_RJF_Cy5.txt.gz 51.0 Mb (ftp)(http) TXT
GSM1085351_slide2_Cy3.txt.gz 26.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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