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Status |
Public on Oct 17, 2014 |
Title |
Aseel 18th day embryo_muscle sample 2 |
Sample type |
RNA |
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Source name |
Muscle of 18th day embryonic stage of Aseel bird
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Organism |
Gallus gallus |
Characteristics |
breed: Aseel tissue: muscle of embryo developmental stage: 18th day embryo
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Treatment protocol |
Embryo of Aseel bird was used as treatment group and embryo of broiler bird was used as control group. Aseel was slow-growing bird while control broiler was fast-growing line.
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Growth protocol |
Chickens were reared following standard managemental protocol at the Institute farm from where fertile eggs were collected. The fertile eggs were kept in the Institute hatchery for embryonic development.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the TRIzol method as recommended by manufacturer's protocol.
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Label |
Cy3
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Label protocol |
The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double-stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis, Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated were determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.
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Hybridization protocol |
600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65ยบ C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).
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Scan protocol |
Scanning was done using Agilent Technologies G2505C scanner.
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Description |
Gene expression at embryonic stage.
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Data processing |
Images were quantified using Feature Extraction Software (Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.
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Submission date |
Oct 16, 2014 |
Last update date |
Oct 17, 2014 |
Contact name |
Tarun K Bhattacharya |
E-mail(s) |
bhattacharyatk@gmail.com
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Organization name |
Directorate of Poultry Research
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Lab |
Molecular Genetics and Breeding
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Street address |
Rajendranagar
|
City |
Hyderabad |
ZIP/Postal code |
500030 |
Country |
India |
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Platform ID |
GPL19304 |
Series (2) |
GSE62444 |
Fold change of expression in Aseel (an indigenous chicken breed) as compared to broiler chicken in muscle of 18th day of embryonic stage |
GSE62445 |
Expression in Aseel (an indigenous chicken breed) as compared to broiler chicken in 7th and 18th days of embryonic stage |
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