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Sample GSM300506 Query DataSets for GSM300506
Status Public on Nov 01, 2008
Title jaw_tcdd_2h_rep3
Sample type RNA
 
Source name jaw, tcdd treated, 2h
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 31.118418
AFFX-BioB-5_at 49.64273
AFFX-BioB-M_at 91.20332
AFFX-BioC-3_at 209.19817
AFFX-BioC-5_at 177.36925
AFFX-BioDn-3_at 968.879
AFFX-BioDn-5_at 645.3673
AFFX-CreX-3_at 7800.6235
AFFX-CreX-5_at 5329.2363
AFFX-DapX-3_at 507.01334
AFFX-DapX-5_at 357.1565
AFFX-DapX-M_at 584.8741
AFFX-Dr-AB076373-1_at 3.6361465
AFFX-Dr-acta1-3_at 12497.262
AFFX-Dr-acta1-5_at 109.526596
AFFX-Dr-acta1-5_x_at 3248.4397
AFFX-Dr-acta1-M_at 5891.7437
AFFX-Dr-AF292559-1_at 3.6418402
AFFX-Dr-AF292559-2_s_at 14.535918
AFFX-Dr-AF292559-3_s_at 7.0085692

Total number of rows: 15617

Table truncated, full table size 401 Kbytes.




Supplementary file Size Download File type/resource
GSM300506.CEL.gz 3.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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