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Sample GSM228889 Query DataSets for GSM228889
Status Public on Sep 12, 2007
Title embryonic hearts, RA treatment, T12h, biological replicate1
Sample type RNA
 
Source name Zebrafish embryonic heart at the age of 84hpf old
Organism Danio rerio
Characteristics Genotype: cmlc2::GFP transgenic zebrafish
Treatment protocol For Retinoic Acid treatment, 72 hpf old zebrafish embryos were treated with 1μM all-trans retinoic acid in 0.1% DMSO or 0.1% DMSO continously until the timepoint for heart extraction. For TCDD treatment, 72 hpf old zebrafish embryos were treated with 1ng/μl TCDD in 0.1% DMSO or 0.1% DMSO as a vehicle control for 1 h.
Growth protocol All zebrafish embryos were kept at 27ºC in egg water with a 14-h/ 10-h light/dark cycle until the designated age for experiment.
Extracted molecule total RNA
Extraction protocol Zebrafish embryonic heart extraction: 200 cmlc2::GFP transgenic embryos were collected in a 1.5 ml Eppendorf tube with 1 ml L-15/10%FBS media and passed through a 19.5 gauge needle connected to a 10 ml syringe 60 times, thus internal organs were separated from the body by shear force. Fluorescent hearts that specifically expressing GFP were identified and picked up under a fluorescence dissecting scope.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Zebrafish Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned in an Aglient Gene Array Scanner
Description Gene expression data of zebrafish embryonic hearts extracted from 84 hpf old embryos at 12 h post RA dosing
Data processing All .cel images were pre-processed with the GC-RMA function in the ArrayAssist Express Version 4.0 software. The output signal intensity for each probeset ID was log2 transformed.
 
Submission date Sep 12, 2007
Last update date Aug 14, 2011
Contact name Jing Chen
E-mail(s) chen12@wisc.edu
Phone 6082624525
Organization name University of Wisconsin - Madison
Department pharmaceutical Sciences
Street address 777 Highland Ave
City Madison
State/province WI
ZIP/Postal code 53705
Country USA
 
Platform ID GPL1319
Series (1)
GSE9020 Comparative Genomics Identifies Gene Targets for Retinoic Acid in the Embryonic Zebrafish Hearts

Data table header descriptions
ID_REF
VALUE Log2 transformed GC-RMA signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-3_at 4.4146934 P 0.011384372
AFFX-BioB-5_at 5.764238 P 0.001247504
AFFX-BioB-M_at 6.4374285 P 7.01E-05
AFFX-BioC-3_at 7.9296365 P 4.43E-05
AFFX-BioC-5_at 7.470084 P 7.01E-05
AFFX-BioDn-3_at 10.363807 P 1.10E-04
AFFX-BioDn-5_at 9.756546 P 4.43E-05
AFFX-CreX-3_at 13.227308 P 4.43E-05
AFFX-CreX-5_at 12.655864 P 4.43E-05
AFFX-DapX-3_at 8.725491 P 7.01E-05
AFFX-DapX-5_at 8.063788 P 1.95E-04
AFFX-DapX-M_at 8.567174 P 5.09E-04
AFFX-Dr-AB076373-1_at 1.9182649 A 0.910595
AFFX-Dr-acta1-3_at 11.615684 P 2.19E-04
AFFX-Dr-acta1-5_at 10.883813 P 9.77E-04
AFFX-Dr-acta1-5_x_at 12.220784 P 2.19E-04
AFFX-Dr-acta1-M_at 11.375794 P 2.66E-04
AFFX-Dr-AF292559-1_at 1.7635368 A 0.098054096
AFFX-Dr-AF292559-2_s_at 3.6477015 A 0.67916995
AFFX-Dr-AF292559-3_s_at 2.7408602 A 0.99641514

Total number of rows: 15617

Table truncated, full table size 588 Kbytes.




Supplementary file Size Download File type/resource
GSM228889.cel.gz 3.4 Mb (ftp)(http) CEL
GSM228889.exp.gz 256 b (ftp)(http) EXP
Raw data provided as supplementary file
Processed data included within Sample table

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