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Sample GSM4321677 Query DataSets for GSM4321677
Status Public on Feb 20, 2020
Title ethanol-6
Sample type RNA
 
Source name embryos
Organism Danio rerio
Characteristics treatment: ethanol
strain: Danio rerio ABTL strain
Treatment protocol Control vs. ethanol-treated zebrafish embryos that were treated from 2 to 4.5 hours postfertilization prior to total RNA being isolated at 4.5 hours postfertilization.
Growth protocol Both treatment groups were grown in embryo medium at 28.5 degrees C, but ethanol-treated zebrafish embryos that grown in 100 mM ethanol from 2 to 4.5 hours postfertilization.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from pools of 20 control and 20 ethanol-treated embryos using TRIzol reagent (Sigma, St Louis, MO, USA). Seven independent experiments were done. RNA samples were purified by passing through the Qiagen RNAeasy column (Cat. No. 74104).
Label biotin
Label protocol Standard protocol for Affymetrix 3' IVT Express kit using 100ng of total RNA
 
Hybridization protocol hybridized for 17h washed and stained on the Affymetrix Fluidics station
Scan protocol Scanned using the Affymetrix 3000 scanner. Data was collected using GCOS software from Affymetrix.
Data processing Affymetrix Gene Expression console was used to generate MAS5 signals, detection calls and detection p-values
 
Submission date Feb 19, 2020
Last update date Feb 20, 2020
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)
GSE145574 Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects

Data table header descriptions
ID_REF
VALUE MAS5 signal, detection call, detection p-value
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 749.9805 P 5.17E-05
AFFX-BioB-M_at 1144.505 P 4.43E-05
AFFX-BioB-3_at 708.3723 P 4.43E-05
AFFX-BioC-5_at 2111.314 P 5.17E-05
AFFX-BioC-3_at 1999.859 P 7.01E-05
AFFX-BioDn-5_at 4312.505 P 4.43E-05
AFFX-BioDn-3_at 6730.899 P 4.43E-05
AFFX-CreX-5_at 21662.43 P 4.43E-05
AFFX-CreX-3_at 28327.08 P 4.43E-05
AFFX-DapX-5_at 1068.354 P 8.14E-05
AFFX-DapX-M_at 1911.118 P 5.17E-05
AFFX-DapX-3_at 3543.018 P 6.02E-05
AFFX-LysX-5_at 145.0148 P 0.000258358
AFFX-LysX-M_at 240.0507 P 7.01E-05
AFFX-LysX-3_at 463.4425 P 7.01E-05
AFFX-PheX-5_at 215.3187 P 0.000509415
AFFX-PheX-M_at 262.9851 P 0.000445901
AFFX-PheX-3_at 507.571 P 0.00010954
AFFX-ThrX-5_at 122.6777 P 0.000753643
AFFX-ThrX-M_at 244.8059 P 0.000581214

Total number of rows: 15617

Table truncated, full table size 590 Kbytes.




Supplementary file Size Download File type/resource
GSM4321677_JR02Z012_Zebrafish_.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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