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Sample GSM300509 Query DataSets for GSM300509
Status Public on Nov 01, 2008
Title jaw_vehicle control_4h_rep3
Sample type RNA
 
Source name jaw, vehicle, 4h
Organism Danio rerio
Characteristics AB wild-type strain
Treatment protocol AB larvae zebrafish were exposed to TCDD (1 ng/ml; TCDD > 99% purity; Chemsyn, Lenexa, KS) or vehicle [0.1% dimethyl sulfoxide (DMSO)] at 96 hpf for 1 h in water and rinsed with fish water. Treatment conditions were limited to 10 embryos or fewer per 1 ml treatment volume. Larvae were raised in 100-mm Petri dishes containing fish water.
Extracted molecule total RNA
Extraction protocol Jaws were microdissected as previously described (Javidan and Schilling, 2004). Larvae were anesthetized with Tricaine-S (Aquatic EcoSystems, Apopka, FL), positioned onto a microscope slide and a drop of Lebovitz’s L15 media + 10% fetal bovine serum (Invitrogen, Carlsbad, CA) was placed onto each specimen. With fine forceps (Fine Science Tools, Foster City, CA) the head (anterior of the pectoral fin) was detached from the body then the eyes and brain tissues were removed. Dissected jaws were placed into a microcentrifuge tube and immediately put into a dry ice bucket. Jaws were stored at -80°C.
Label biotin
Label protocol The One-Cycle Target Labeling and Control Reagents kit was used to synthesize cDNA and biotinylated cRNA following the manufacturer’s protocol (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Biotin-labeled cRNA (15 µg) was fragmented and hybridized onto Affymetrix Zebrafish Genechip Arrays following the protocol in the Affymetrix Genechip Expression Analysis Technical Manual.
Scan protocol Following hybdrization, the arrays were washed and stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400 using the protocol EukGE WS2v4. Arrays were scanned with an Agilent Gene Array Scanner.
Description no additional information
Data processing Analysis of the relative abundance of each gene transcript was determined using Arrayassist microarray software (Stratagene, La Jolla, CA). In brief, .CHP files were uploaded into the software and probe intensities were corrected for background noise and normalized across all array replicates with the GC-Robust Multi-Array Average (GC-RMA) algorithm. Expression levels for each transcript were log2-transformed, and the average log2 value for the TCDD samples was compared to the average value for the DMSO replicates. Those transcripts that were altered by TCDD by at least 2 fold over DMSO at any of the time points (p < 0.05) were selected for further analysis. Significant changes were determined by an unpaired t-test.
 
Submission date Jun 26, 2008
Last update date Jun 27, 2008
Contact name Kong M Xiong
Organization name University of Wisconsin at Madison
Department Biomolecular Chemistry
Lab Heideman/Peterson Fish Group
Street address 777 Highland Ave, 5208 Rennebohm Hall
City Madison
State/province WI
ZIP/Postal code 53705
Country USA
 
Platform ID GPL1319
Series (1)
GSE11893 AHR Activation by TCDD Downregulates Sox9b Expression Producing Jaw Malformation in Zebrafish Embryos

Data table header descriptions
ID_REF
VALUE GC-RMA signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 58.053673
AFFX-BioB-5_at 103.15935
AFFX-BioB-M_at 157.41664
AFFX-BioC-3_at 295.7276
AFFX-BioC-5_at 290.7691
AFFX-BioDn-3_at 1573.9327
AFFX-BioDn-5_at 1006.0088
AFFX-CreX-3_at 8137.908
AFFX-CreX-5_at 6484.3853
AFFX-DapX-3_at 376.397
AFFX-DapX-5_at 265.0659
AFFX-DapX-M_at 327.71014
AFFX-Dr-AB076373-1_at 3.9366727
AFFX-Dr-acta1-3_at 9308.671
AFFX-Dr-acta1-5_at 59.474304
AFFX-Dr-acta1-5_x_at 3485.4932
AFFX-Dr-acta1-M_at 4679.475
AFFX-Dr-AF292559-1_at 3.6183376
AFFX-Dr-AF292559-2_s_at 11.85752
AFFX-Dr-AF292559-3_s_at 6.403409

Total number of rows: 15617

Table truncated, full table size 401 Kbytes.




Supplementary file Size Download File type/resource
GSM300509.CEL.gz 3.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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