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Sample GSM877082 Query DataSets for GSM877082
Status Public on Feb 18, 2012
Title wild-type zebrafish, biological rep2
Sample type RNA
 
Source name upper digestive tract tissue from 3 wild-type zebrafish
Organism Danio rerio
Characteristics tissue: upper digestive tract
genetic background: AB
age: 3 months
genotype: wild-type
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)
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
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.
Label biotin
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).
 
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).
Scan protocol Arrays were scanned with the GeneArray G7 scanner (Affymetrix) to obtain image and signal intensities
Description Gene expression data from upper digestive tract tissue of 3 wild-type zebrafish
Data processing Data analysis was performed using the Affymetrix MAS5 algorithm.
 
Submission date Feb 16, 2012
Last update date Feb 18, 2012
Contact name Hao Chen
E-mail(s) chenh@nccu.edu
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
 
Platform ID GPL1319
Series (1)
GSE35889 Expression data from adult wild-type and zCdx1b transgenic zebrafish (3 months old)

Data table header descriptions
ID_REF
VALUE log2 MAS 5.0 signal

Data table
ID_REF VALUE
AFFX-BioB-3_at 6.12815
AFFX-BioB-5_at 6.60674
AFFX-BioB-M_at 7.24955
AFFX-BioC-3_at 8.3281
AFFX-BioC-5_at 8.40055
AFFX-BioDn-3_at 11.0499
AFFX-BioDn-5_at 9.43712
AFFX-CreX-3_at 12.452
AFFX-CreX-5_at 12.0953
AFFX-DapX-3_at 2.74768
AFFX-DapX-5_at 2.87112
AFFX-DapX-M_at 2.98488
AFFX-Dr-AB076373-1_at 3.05087
AFFX-Dr-AF292559-1_at 3.23818
AFFX-Dr-AF292559-2_s_at 3.36206
AFFX-Dr-AF292559-3_s_at 3.80156
AFFX-Dr-AF292559-4_s_at 2.88024
AFFX-Dr-AF292560-1_s_at 3.0216
AFFX-Dr-AF298789-1_at 3.24916
AFFX-Dr-AF323980-1_at 3.12012

Total number of rows: 15617

Table truncated, full table size 375 Kbytes.




Supplementary file Size Download File type/resource
GSM877082_W7_Zebrafish_.CEL.gz 1.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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