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Series GSE9746 Query DataSets for GSE9746
Status Public on Dec 07, 2007
Title Whole Daphnia_20microg/L Cadmium_48hr
Organism Daphnia pulex
Experiment type Expression profiling by array
Summary "Gene response profiles for Daphnia pulex exposed to the environmental stressor cadmium reveals novel crustacean metallothioneins." Joseph.R.Shaw, John.K.Colbourne, Jennifer.C.Davey, Stephen.P.Glaholt, Thomas.H.Hampton, Celia.Y.Chen, Carol.L.Folt, Joshua.W.Hamilton (BMC Genomics 2007).

Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.

Our microarray identified genes reported in the literature to be regulated in response to cadmium exposure, suggested functional attributes for genes that share no sequence similarity to proteins in the public databases, and pointed to genes that are likely members of expanded gene families in the Daphnia genome. Genes identified on the microarray also were associated with cadmium induced phenotypes and population-level outcomes that we experimentally determined. A subset of genes regulated in response to cadmium exposure was independently validated using quantitative-realtime (Q-RT)-PCR. These microarray studies led to the discovery of three genes coding for the metal detoxication protein metallothionein (MT). The gene structures and predicted translated sequences of D. pulex MTs clearly place them in this gene family. Yet, they share little homology with previously characterized MTs.

The genomic information obtained from this study represents an important first step in characterizing microarray patterns that may be diagnostic to specific environmental contaminants and give insights into their toxicological mechanisms, while also providing a practical tool for evolutionary, ecological, and toxicological functional gene discovery studies. Advances in Daphnia genomics will enable the further development of this species as a model organism for the environmental sciences.
Keywords: cDNA microarrays, stress response, expressed sequence tags (EST), Daphnia Genomics Consortium, Arthropod, Gene Expression Profiling, Gene Expression Regulation
 
Overall design Microarrays were used to discover genes that were differentially expressed following sub-lethal cadmium exposure (LC01; 20microg/L, 48-h) in D. pulex. They utilized RNA isolated from three independent and concurrently replicated exposures of Daphnia to cadmium and control conditions. RNA was applied to three microarrays using a standard, control vs. treated design that included dye swaps.
 
Contributor(s) Shaw JR, Colbourne JK, Davey JC, Glaholt SP, Hampton TH, Chen CY, Folt CL, Hamilton JW
Citation(s) 18154678
Submission date Dec 02, 2007
Last update date Jun 06, 2019
Contact name Joseph R Shaw
E-mail(s) joeshaw@indiana.edu
Organization name Indiana University
Department The School of Public and Environmental Affairs
Lab Shaw Lab
Street address 1315 E. Tenth Street
City Bloomington
State/province IN
ZIP/Postal code 47405
Country USA
 
Platforms (1)
GPL6195 IU/UNH/DU Daphnia pulex Generation 2.4 (3.1K)
Samples (3)
GSM246093 Whole Daphnia_20microg/LCadmium_48hr_rep1
GSM246094 Whole Daphnia_20microg/LCadmium_48hr_rep2
GSM246095 Whole Daphnia_20microg/LCadmium_48hr_rep3
Relations
BioProject PRJNA103667

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9746_RAW.tar 2.5 Mb (http)(custom) TAR (of GPR, TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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