{"database": "metadata", "table": "run_metadata", "rows": [[36488, "SRR530888", "SRX172592", "SRS352614", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "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 hpf and measured microRNA expression using several methods at 36 hpf 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: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "36hpf TCDD 3", "GSM979602", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD", "36hpf TCDD 3", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD", "GSM979602", "GSM979602: 36hpf TCDD 3; Danio rerio; RNA Seq", "GSM979602 1", "GSM979602: 36hpf TCDD 3", "1", null, "GEO Accession:GSM979602", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "350Application ReadForward1", "SRP014646", null, null, "MH_0006.qual MH_0006.csfasta", "SOLiD_native SOLiD_native", 214059615.0, 6115989.0, "GSM979602 r1", "0:35", "0:56635752;1:54053300;2:48355842;3:54677354;.:337367", 35, null, null, null, null, null, null, null, null, "SRX172592", "SRS352614", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.13044, null, 0.07694, null, 0.95704, null, 0.53005, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["36488"], "units": {}, "query_ms": 12.516597998910584}