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Sample GSM3816726 Query DataSets for GSM3816726
Status Public on May 25, 2019
Title Whole Red Blood Cells Sample 38803 BCD
Sample type genomic
 
Source name whole red blood cells
Organism Gallus gallus
Characteristics line: Cross BCD
gender: male
developmental stage: 46 days post-hatch
Treatment protocol none
Growth protocol Animal experiments for crossbred (BCD) and purebred chickens (B and C) are described in studies by Zhou et al. (Zhou, N., Lee, W.R. and Abasht, B., 2015. Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens’ feed efficiency. BMC genomics, 16(1), p.195.) and Mutryn et al. (Mutryn, M.F., Brannick, E.M., Fu, W., Lee, W.R. and Abasht, B., 2015. Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing. BMC genomics, 16(1), p.399.), respectively.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from whole blood using DNeasy Blood & Tissue Kit (Qiagen)
Label biotin
Label protocol Performed by Neogen following manufacturers specification (Affymetrix) using a Biomek FX robot, the DNA was amplified, fragmented and purified to create a hybridization ready (hyb-ready) mixture.
 
Hybridization protocol Performed by Neogen following manufactures specification (Affymetrix), the hyb-ready DNA mixture was transferred to a GeneTital Multi-Channel instrument for automated processing of the hybridization step.
Scan protocol Arrays were processed and imaged using a Affymetrix Gene Titan Multi-Channel (MC) Instrument by Neogen following manufacturers instructions
Data processing Raw cell files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 (Axiom_GW_GT_Chicken.na35.annot.db) using the software's Best Practices for Agricultural animals and a VCF file exported for all SNPs.
 
Submission date May 24, 2019
Last update date May 25, 2019
Contact name Behnam Abasht
E-mail(s) abasht@udel.edu
Phone 302-831-8876
Organization name University of Delaware
Department Animal and Food Sciences
Lab Abasht Laboratory
Street address 531 South College Avenue
City Newark
State/province DE
ZIP/Postal code 19716
Country USA
 
Platform ID GPL23815
Series (1)
GSE131764 Axiom Genome-Wide Chicken Array of Broiler Chickens

Supplementary file Size Download File type/resource
GSM3816726_38803.CEL.gz 12.2 Mb (ftp)(http) CEL
Processed data are available on Series record

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