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Series GSE38839 Query DataSets for GSE38839
Status Public on Aug 02, 2012
Title MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos [agilent and exiqon array data]
Platform organisms Danio rerio; Homo sapiens; Mus musculus; Rattus norvegicus; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Betapolyomavirus hominis; Betapolyomavirus macacae
Sample organism Danio rerio
Experiment type Non-coding RNA profiling by array
Summary Although many drugs and environmental chemicals are teratogenic, the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs (miRNAs), single-stranded RNA molecules of ~22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation, are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well-known teratogen, we exposed zebrafish embryos to DMSO (0.1%) or TCDD (5 nM) for 1 hr at 30 hours post fertilization (hpf) and measured microRNA expression using several methods at 36 and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf (62-fold) and 60 hpf (135-fold) as determined by qPCR, verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays (Agilent and Exiqon), next-generation sequencing (SOLiD) and real time RT-PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR-451, 23a, 23b, 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However, miR-27e was the only miRNA to be identified as differentially expressed by all three methods (both microarrays, SOLiD sequencing, and qPCR). These results suggest that TCDD exposure causes modest changes in expression of microRNAs, including some (miR-451, 23a, 23b, 24 and 27e) that are critical for hematopoiesis and cardiovascular development.
 
Overall design MicroRNA profiling was performed (N=3 biological replicates per group) using custom designed Agilent miRNA microarrays (8x15K) and exiqon miRCURY LNA microarrays. Custom-made Agilent oligonucleotide miRNA microarrays were designed based on zebrafish mature miRNA sequences from miRbase v.16. Each individual array contained a total of 548 unique probes representing 259 mature miRNAs from zebrafish (245), Fugu rubripes (11) and Tetraodon nigriviridis (3). Exiqon miRNA probes were based on zebrafish miRNA sequences from miRbase v. 12.
 
Contributor(s) Jenny MJ, Aluru N, Hahn ME
Citation(s)
  • Jenny MJ, Aluru N, Hahn ME. Effects of short-term exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin on microRNA expression in zebrafish embryos. Toxicol Appl Pharmacol 2012 Oct 15;264(2):262-73. PMID: 22921993
Submission date Jun 20, 2012
Last update date Nov 01, 2012
Contact name Neelakanteswar Aluru
E-mail(s) naluru@whoi.edu
Phone 508-289-3607
Organization name Woods Hole Oceanographic Institution
Department Biology
Lab Aluru Lab
Street address 45 Water Street
City Woods Hole
State/province MA
ZIP/Postal code 02543
Country USA
 
Platforms (2)
GPL7724 miRCURY LNA microRNA Array, v. 9.2, all organisms
GPL15720 8x15K custom made zebrafish miRNA microarray [Agilent-024479]
Samples (24)
GSM979539 36_DMSO_1 [agilent]
GSM979540 36_DMSO_2 [agilent]
GSM979541 36_DMSO_3 [agilent]
This SubSeries is part of SuperSeries:
GSE39809 MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos
Relations
BioProject PRJNA171750

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
GSE38839_RAW.tar 30.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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