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Sample GSM1129300 Query DataSets for GSM1129300
Status Public on Sep 01, 2013
Title Prim-5_0.625mM MTBE, bio rep 3
Sample type RNA
 
Source name embryo at Prim-5_exposed to 0.625mM MTBE
Organism Danio rerio
Characteristics tissue: whole embryo lysate
genotype: Tg(fli1a:EGFP)y1
developmental stage: Prim-5; ~30hpf
exposed to: 0.625mM MTBE
Treatment protocol Staged (1K cell stage) embryos were randomly assiged to a experimental group consisting of a time point and treatment. Each group consisted of 15 embryos which were pooled for 1 experimental replicate, with three replicates for each experimental group. Treatment with 0.00625, 0.625, 5mM MTBE or control was in a sealed glass vial beginning at approximately 3 hours post fertilization and ending at the assigned time point. Upon completion of the exposure, embryos were snap frozen in liquid nitrogen and stored at -80C until RNA was extracted.
Growth protocol Embryos were maintained at 25C for the duration of exposure.
Extracted molecule total RNA
Extraction protocol RNA extractions: RNeasy Mini Kit 250 (p/n 74106) with on-column DNase treatment (RNAse-free DNAse set, 50 rxn, p/n 79254); Reverse transcription and amplification: NuGEN WT-Ovation™ Pico System (p/n 3300-60); cDNA cleanup by Zymo Research DNA Clean & Concentrator -25 kit (p/n D4006).
Label biotin
Label protocol Fragmentation and biotinylation: NuGEN Encore™ Biotin Module (p/n 4200-60) according to the manufacturer.
 
Hybridization protocol Hybridizations were performed in an Affymetrix GeneChip Hybridization Oven 640, washing and staining on the Affymetrix Fluidics Station 450 using the GCOS software and protocol EukGE-WS2V4_450.
Scan protocol Scanning on the Affymetrix GeneChip Scanner using GCOS software and according to standard Affymetrix protocols.
Description 30_MC.CEL
gene expression of zebrafish embryos exposed to 0.625mM MTBE and collected at Prim-5
Data processing Agilent Technologies GeneSpring GX software
 
Submission date Apr 25, 2013
Last update date Sep 01, 2013
Contact name Josephine Ann Bonventre
Organization name Oregon State University
Department Environmental & Molecular Toxicology
Lab Harper
Street address 1011 Agriculture & Life Sciences Building
City Corvallis
State/province OR
ZIP/Postal code 97331
Country USA
 
Platform ID GPL1319
Series (1)
GSE46371 Expression data from zebrafish (Danio rerio) embryos exposed to methyl tert-butyl ether

Data table header descriptions
ID_REF
VALUE log2 RMA

Data table
ID_REF VALUE
Dr.1448.1.S1_at 9.838836
Dr.20010.7.S1_at 9.241916
Dr.23067.1.S1_at 10.574695
Dr.2914.1.S2_at 8.961245
Dr.26411.1.S1_a_at 6.492741
Dr.815.1.S1_x_at 10.344661
Dr.4812.1.S1_s_at 11.09266
DrAffx.2.19.S1_at 8.820103
AFFX-Dr-acta1-3_at 10.761875
Dr.20097.1.S1_s_at 8.1454
Dr.8472.1.S1_at 9.613452
AFFX-Dr-acta1-M_at 9.323892
Dr.815.1.S1_at 10.271255
Dr.26411.1.S1_at 7.548209
Dr.2914.1.S1_at 8.512116
Dr.1450.1.S1_at 9.430903
Dr.23788.3.S1_at 7.75363
Dr.24260.1.S1_at 9.014451
Dr.5549.1.S1_at 8.279077
Dr.13868.1.S1_at 8.155748

Total number of rows: 15617

Table truncated, full table size 391 Kbytes.




Supplementary file Size Download File type/resource
GSM1129300_30_MC.CEL.gz 1.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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