NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM300507 Query DataSets for GSM300507
Status Public on Nov 01, 2008
Title jaw_vehicle control_4h_rep1
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 47.97877
AFFX-BioB-5_at 107.332886
AFFX-BioB-M_at 139.23734
AFFX-BioC-3_at 259.16238
AFFX-BioC-5_at 284.19525
AFFX-BioDn-3_at 1608.2336
AFFX-BioDn-5_at 988.1057
AFFX-CreX-3_at 8024.3516
AFFX-CreX-5_at 6417.08
AFFX-DapX-3_at 269.10675
AFFX-DapX-5_at 205.74545
AFFX-DapX-M_at 214.2955
AFFX-Dr-AB076373-1_at 4.624387
AFFX-Dr-acta1-3_at 8963.637
AFFX-Dr-acta1-5_at 50.67887
AFFX-Dr-acta1-5_x_at 4458.0767
AFFX-Dr-acta1-M_at 5490.3223
AFFX-Dr-AF292559-1_at 4.0313787
AFFX-Dr-AF292559-2_s_at 18.938408
AFFX-Dr-AF292559-3_s_at 8.007035

Total number of rows: 15617

Table truncated, full table size 401 Kbytes.




Supplementary file Size Download File type/resource
GSM300507.CEL.gz 3.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap