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Series GSE52873 Query DataSets for GSE52873
Status Public on Dec 03, 2013
Title Microarray data from zebrafish embryos (ZFE) exposed for 48-hr periods to oil emulsions collected from GoM shoreline sites following the Deepwater Horizon blowout.
Organism Danio rerio
Experiment type Expression profiling by array
Summary Zebrafish embryos/larvae are a choice model system for studying early stages of vertebrate development and how these stages can be perturbed by environmental stressors. Petrochemical combustion products elicit developmental toxicity that is associated with transcriptome changes in zebrafish embryos (ZFE). We used microarrays to characterize transcriptome changes in ZFE that had been exposed in the laboratory to oil emulsions collected from the GoM shoreline, ~9 weeks after the Deepwater Horizon blowout.
Overall design ZFE were exposed to oil emulsions collected (July 1-4, 2010) at the shoreline in Gulfport, MS, Fort Morgan, AL and Perdido Key, FL. ZFE were exposed to emulsions, consisting of varying amounts of alkanes, polynuclear aromatic hydrocarbons (PAHs), sand and seawater that had been “buttered” on the bottom of cups, in which ZFE were suspended in zebrafish medium. ZFE development was monitored by light microscopy.  Control ZFE were suspended in zebrafish medium without emulsions. Gross developmental abnormalities, including axial changes, altered swimming patterns and yolk sac and pericardial sac swelling were noted and photographed.   ZFE were collected at 48-hr intervals, after exposures had begun, and either placed in clean medium for up to 48 hours more, or, were collected immediately for RNA extraction. and hybridization on Affymetrix zebrafish microarrays, each containing 14,900 probe sets. We extracted RNA from all 30 ZFE in each cup for microarray analysis.
Contributor(s) Penn A, Kleinow K, Xin F, Bui A, Xiao R, Perveen Z, Polk P
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Submission date Dec 02, 2013
Last update date Jan 25, 2018
Contact name Rui Xiao
Organization name Columbia University
Department Anesthesiology
Lab P&S 12-402
Street address 630 West 168th Street
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platforms (1)
GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array
Samples (11)
GSM1277367 ZebrafishEmbyos_Control~72_rep1
GSM1277368 ZebrafishEmbyos_Control~72_rep2
GSM1277369 ZebrafishEmbyos_Control~72_rep3
BioProject PRJNA230381

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Supplementary file Size Download File type/resource
GSE52873_RAW.tar 23.0 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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