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Sample GSM1176784 Query DataSets for GSM1176784
Status Public on Jul 09, 2014
Title control_rep4
Sample type RNA
 
Source name Total RNA from control embryos
Organism Danio rerio
Characteristics strain: TL
age: 8 hours postfertilization
tissue: whole body
treatment: control
treatment duration: 6 hrs
Treatment protocol Embryos were exposed to ethanol by incubation in embryo medium containing 100 mM (0.6% vol./vol.) ethanol from 2 hours post fertilization (hpf) until the completion of the experiment, in Petri dishes wrapped with parafilm and maintained at 28.5ºC.
Growth protocol Embryos were grown by incubation in embryo medium, in Petri dishes wrapped with parafilm and maintained at 28.5ºC.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from approximately 20 treated and untreated embryos at 8 hpf using TRIzol reagent (Sigma, St. Louis, MO USA).
Label Biotin
Label protocol Total RNA was labeled using the 3' IVT express kit from Affymetrix.
 
Hybridization protocol Affymetrix standard protocol, except hybridization for 17 hours.
Scan protocol Scanned using 3000-7G controlled by Affymetrix GCOS.
Description Gene expression data from control embryos.
Data processing Affymetrix MAS5 data scaled to intensity of 1000.
 
Submission date Jun 27, 2013
Last update date Jul 09, 2014
Contact name James A Marrs
E-mail(s) jmarrs@iupui.edu
Organization name Indiana University-Purdue University Indianapolis
Department Biology
Lab SL328
Street address 723 West Michigan Street
City Indianapolis
State/province IN
ZIP/Postal code 46202
Country USA
 
Platform ID GPL1319
Series (1)
GSE48380 Ethanol exposure disrupts extraembryonic microtubule cytoskeleton and embryonic blastomere cell adhesion, producing epiboly and gastrulation defects

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 1192.91 P 0.000146581
AFFX-BioB-M_at 1877.67 P 4.42873e-05
AFFX-BioB-3_at 1226.48 P 4.42873e-05
AFFX-BioC-5_at 3372.75 P 5.16732e-05
AFFX-BioC-3_at 3779.42 P 8.14279e-05
AFFX-BioDn-5_at 9625.95 P 4.42873e-05
AFFX-BioDn-3_at 13990.9 P 4.42873e-05
AFFX-CreX-5_at 56770.8 P 4.42873e-05
AFFX-CreX-3_at 80180.1 P 4.42873e-05
AFFX-DapX-5_at 1067.05 P 0.00022441
AFFX-DapX-M_at 2340.41 P 8.14279e-05
AFFX-DapX-3_at 4154.7 P 4.42873e-05
AFFX-LysX-5_at 216.65 P 0.00499495
AFFX-LysX-M_at 355.886 P 0.00401721
AFFX-LysX-3_at 502.638 P 4.42873e-05
AFFX-PheX-5_at 248.635 P 0.000445439
AFFX-PheX-M_at 263.592 P 0.000662269
AFFX-PheX-3_at 517.241 P 0.00158993
AFFX-ThrX-5_at 184.795 M 0.054198
AFFX-ThrX-M_at 206.034 A 0.0894781

Total number of rows: 15617

Table truncated, full table size 562 Kbytes.




Supplementary file Size Download File type/resource
GSM1176784_JR01Z007_Zebrafish.CEL.gz 1.4 Mb (ftp)(http) CEL
GSM1176784_JR01Z007_Zebrafish.mas5.CHP.gz 97.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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