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Status |
Public on Feb 18, 2012 |
Title |
wild-type zebrafish, biological rep2 |
Sample type |
RNA |
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Source name |
upper digestive tract tissue from 3 wild-type zebrafish
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Organism |
Danio rerio |
Characteristics |
tissue: upper digestive tract genetic background: AB age: 3 months genotype: wild-type
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Treatment protocol |
Transgenic zebrafish were generated by microinjection of one cell stage fertilized AB* zebrafish eggs with a mixture of pmini Tol2-zK5p-zCdx1b-EGFP (80µg/ml) and Tol2 transposase RNA (4 µg/ml)
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Growth protocol |
Zebrafish were obtained from the Zebrafish International Resource Center (Eugene, OR). To generate zCdx1b transgenic fish, AB* line was used. Fish were housed in an automatic fish housing system (Aquaneering, San Diego, CA) at 28.5°C and maintained according to the established procedures
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Extracted molecule |
total RNA |
Extraction protocol |
The upper digestive tract tissue from 3 adult zebrafish (3 months old) was dissected and pooled as one sample. Three zCdx1b transgenic samples were used for microarray, and 2 wild type samples were used for control. The total RNA was extracted using TRIzol according to the manufacturer's instructions.
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Label |
biotin
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Label protocol |
Biotinylated cRNAs were generated from cDNAs by in vitro transcription and amplified by using the BioArray T7 RNA polymerase labeling kit (Enzo Diagnostics).
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Hybridization protocol |
After purification of cRNAs by GeneChip Sample Cleanup Module (Affymetrix), 15 µg of cRNA was fragmented at 94°C for 35 min. Approximately 12.5 µg of fragmented cRNA was used in a 250-µl hybridization mixture containing herring-sperm DNA (0.1 mg/ml; Promega), plus bacterial and phage cRNA controls (1.5 pM BioB, 5 pM BioC, 25 pM BioD, and 100 pM Cre) to serve as internal controls for hybridization efficiency. Aliquots (200 µl) of the mixture were hybridized to arrays for 16 h at 45°C in a GeneChip Hybridization Oven 640 (Affymetrix). Each array was washed and stained with streptavidin–phycoerythrin (Invitrogen) and amplified with biotinylated anti-streptavidin antibody (Vector Laboratories) on the GeneChip Fluidics Station 450 (Affymetrix).
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Scan protocol |
Arrays were scanned with the GeneArray G7 scanner (Affymetrix) to obtain image and signal intensities
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Description |
Gene expression data from upper digestive tract tissue of 3 wild-type zebrafish
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Data processing |
Data analysis was performed using the Affymetrix MAS5 algorithm.
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Submission date |
Feb 16, 2012 |
Last update date |
Feb 18, 2012 |
Contact name |
Hao Chen |
E-mail(s) |
chenh@nccu.edu
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Organization name |
North Carolina Central University
|
Department |
BBRI
|
Lab |
Xiaoxin Luke Chen's Lab
|
Street address |
700 George Street
|
City |
Durham |
ZIP/Postal code |
27707 |
Country |
USA |
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Platform ID |
GPL1319 |
Series (1) |
GSE35889 |
Expression data from adult wild-type and zCdx1b transgenic zebrafish (3 months old) |
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