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| Status |
Public on May 25, 2019 |
| Title |
Whole Red Blood Cells Sample 13815 BCD |
| Sample type |
genomic |
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| Source name |
whole red blood cells
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| Organism |
Gallus gallus |
| Characteristics |
line: Cross BCD
gender: male
developmental stage: 46 days post-hatch
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| Treatment protocol |
none
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| 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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from whole blood using DNeasy Blood & Tissue Kit (Qiagen)
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| Label |
biotin
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| 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.
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| 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.
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| Scan protocol |
Arrays were processed and imaged using a Affymetrix Gene Titan Multi-Channel (MC) Instrument by Neogen following manufacturers instructions
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| 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.
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| Submission date |
May 24, 2019 |
| Last update date |
May 25, 2019 |
| Contact name |
Behnam Abasht |
| E-mail(s) |
abasht@udel.edu
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| Phone |
302-831-8876
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| Organization name |
University of Delaware
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| Department |
Animal and Food Sciences
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| Lab |
Abasht Laboratory
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| Street address |
531 South College Avenue
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| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19716 |
| Country |
USA |
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| Platform ID |
GPL23815 |
| Series (1) |
| GSE131764 |
Axiom Genome-Wide Chicken Array of Broiler Chickens |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM3816710_13815.CEL.gz |
12.3 Mb |
(ftp)(http) |
CEL |
| Processed data are available on Series record |
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