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Series GSE82318 Query DataSets for GSE82318
Status Public on Aug 27, 2016
Title Epigenetic Programming Alterations in Alligators from Environmentally Contaminated Lakes
Organism Alligator mississippiensis
Experiment type Methylation profiling by genome tiling array
Summary Previous studies examining the reproductive health of alligators in Florida lakes indicate that a variety of developmental and health impacts can be attributed to environmental quality and exposures to environmental contaminants. A number of these environmental contaminants have been shown to disrupt normal endocrine signaling. The potential that these environmental toxicants may influence epigenetic status and correlate to the health abnormalities was investigated in the current study. The red blood cell (RBC) (erythrocyte) in the alligator is nucleated so was used as an easily purified marker cell to investigate epigenetic programming. RBCs were collected from adult male alligators captured at three sites in Florida, each characterized by varying degrees of contamination. While Lake Woodruff (WO) has remained relatively pristine, Lake Apopka (AP) and Merritt Island (MI) convey exposures to different suites of contaminants. DNA was isolated and methylated DNA immunoprecipitation (MeDIP) was used to isolate methylated DNA that was then analyzed in a competitive hybridization using a genome-wide alligator tiling array for a MeDIP-Chip analysis. Pairwise comparisons of alligators from AP and MI to WO revealed alterations in the DNA methylome. The AP vs. WO comparison identified 85 differential DNA methylation regions (DMRs) with ≥3 adjacent oligonucleotide tiling array probes and 15,451 DMRs with a single oligo probe analysis. The MI vs. WO comparison identified 75 DMRs with the ≥3 oligo probe and 17,411 DMRs with the single oligo probe analysis. There was negligible overlap between the DMRs identified in AP vs. WO and MI vs. WO comparisons. In both comparisons DMRs were primarily associated with CpG deserts which are regions of low CpG density (1-2 CpG/100bp). Although the alligator genome is not fully annotated, gene associations were identified and correlated to major gene functional categories and pathways. Observations demonstrate that environmental quality is associated with epigenetic programming and status in the alligator. The epigenetic alterations may provide biomarkers to assess the environmental exposures and health impacts on these populations of alligators.
 
Overall design The current study was designed to investigate potential alterations in the epigenome of alligators living in contaminated and non-contaminated lakes in Florida. The experimental design involved the collection of blood samples from adult male alligators from Lake Apopka and Merritt Island National Wildlife Refuge as contaminated lakes and Lake Woodruff as a reference lake. The epigenome analysis in the RBC involved the isolation of DNA followed by a methylated DNA immunoprecipitation (MeDIP). The MeDIP was then analyzed using a genome-wide alligator tiling array chip set (Chip) to identify differential DNA methylation regions (DMRs). Comparative hybridizations between the Lake Apopka alligator samples versus Lake Woodruff alligator samples and Merritt Island National Wildlife Refuge alligator versus Lake Woodruff alligator samples were made with two independent experiments with different sets of multiple animals from each site.
 
Contributor(s) Guillette LJ Jr, Parrott BB, Nilsson E, Haque MM, Skinner MK
Citation(s) 27080547
Submission date Jun 06, 2016
Last update date Nov 28, 2016
Contact name Michael K Skinner
E-mail(s) skinner@mail.wsu.edu
Organization name WSU
Department SBS
Street address Abelson 507
City Pullman
State/province WA
ZIP/Postal code 99163
Country USA
 
Platforms (1)
GPL21985 121211-allmis-ms-meth-ux1
Samples (4)
GSM2293612 [AP/WO]-[array1]
GSM2293613 [MI/WO]-[array1]
GSM2293614 [AP/WO]-[array2]
Relations
BioProject PRJNA340260

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
GSE82318_RAW.tar 1.1 Gb (http)(custom) TAR (of XYS)
GSE82318_RegionsCombined_APvsWO_1e-4_500_3.pd.121211.allmis1.2of2.ms.meth.ux1.csv.gz 495.2 Kb (ftp)(http) CSV
GSE82318_RegionsCombined_MIvsWO_1e-4_500_3.pd.121211.allmis1.1of2.ms.meth.ux1.csv.gz 557.9 Kb (ftp)(http) CSV
GSE82318_RegionsCombined_MIvsWO_1e-5_500_3.pd.121211.allmis1.1of2.ms.meth.ux1.csv.gz 270.4 Kb (ftp)(http) CSV
Raw data provided as supplementary file
Processed data are available on Series record

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