Series Summary for DCD000337SR

Transcriptomic analyses of TCDD treated zebrafish liver

Case Control

10.1371/journal.pone.0077292

GSE49915

TCDD is one of the most persistent environmental toxicants in biological systems and its effect through aryl hydrocarbon receptor (AhR) has been well characterized. However, the information on TCDD-induced toxicity in other molecular pathways is rather limited. To fully understand molecular toxicity of TCDD in an in vivo animal model, adult zebrafish were exposed to TCDD at 10 nM for 96 h and the livers were sampled for RNA-sequencing based transcriptomic profiling. A total of 1,058 differently expressed genes were identified based on fold-change>2 and TPM (transcripts per million) >10. Among the top 20 up-regulated genes, 10 novel responsive genes were identified and verified by RT-qPCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle, endocrine disruptors, signal transduction and immune systems. Comparative analyses of TCDD-induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up-regulated while calcium signaling pathway and several immune-related pathways are generally down-regulated. Finally, our study also suggested that zebrafish model showed greater similarity to in vivo mammalian models than in vitro models. Our study indicated that the zebrafish is a valuable in vivo model in toxicogenomic analyses for understanding molecular toxicity of environmental toxicants relevant to human health. The expression profiles associated with TCDD could be useful for monitoring environmental dioxin and dioxin-like contamination.

True

mickael.dong

June 1, 2017, 5:25 a.m.

Oct. 23, 2018, 12:46 a.m.

Assays

Biosample ID Series biosample_type biosample_lab genetic_background stage Anatomical Term Hours Post Fertilization
DCD006941BS DCD000337SR tissue Gong Lab, National University of Singapore SING 90 Days-2 Years liver adult
Applied Assay ID Biosample Replicate Assay
DCD001926AA DCD013453BR small-RNA-seq_Gong_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002277SQ DCD002284TR Gong Lab, National University of Singapore SOLiD AB SOLiD System unstranded 11/12/2013
DCD004748DT: FASTQ
DCD008837DT: BIGWIG GRCz10/danRer10
DCD009480DT: LOG GRCz10/danRer10
DCD009481DT: TSV GRCz10/danRer10
DCD009482DT: TSV GRCz10/danRer10
DCD009483DT: BEDGRAPH GRCz10/danRer10
DCD009484DT: BEDGRAPH GRCz10/danRer10
DCD009485DT: BEDGRAPH GRCz10/danRer10
DCD009486DT: PDF GRCz10/danRer10
DCD009487DT: LOG GRCz10/danRer10
DCD009488DT: BEDGRAPH GRCz10/danRer10
DCD009489DT: LOG GRCz10/danRer10
DCD009490DT: PDF GRCz10/danRer10
DCD009495DT: BAM GRCz10/danRer10
DCD015901DT: LOG GRCz11/danRer11
DCD015902DT: TSV GRCz11/danRer11
DCD015903DT: TSV GRCz11/danRer11
DCD015904DT: BEDGRAPH GRCz11/danRer11
DCD015905DT: BIGWIG GRCz11/danRer11
DCD015906DT: PDF GRCz11/danRer11
DCD015907DT: LOG GRCz11/danRer11
DCD015908DT: PDF GRCz11/danRer11
DCD015909DT: LOG GRCz11/danRer11
DCD015915DT: BEDGRAPH GRCz11/danRer11
DCD015935DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Controlled By Anatomical Term Treatment Hours Post Fertilization Mutation Description
DCD006942BS DCD000337SR tissue Gong Lab, National University of Singapore SING 90 Days-2 Years liver adult
Applied Assay ID Biosample Replicate Assay Controlled By
DCD001925AA DCD013454BR small-RNA-seq_Gong_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Chemistry Version Paired End Strand Maximum Read Length Sequencing Date
DCD002276SQ DCD002283TR Gong Lab, National University of Singapore SOLiD AB SOLiD System unstranded 11/12/2013
DCD004747DT: FASTQ
DCD008832DT: BIGWIG GRCz10/danRer10
DCD009527DT: LOG GRCz10/danRer10
DCD009528DT: TSV GRCz10/danRer10
DCD009529DT: TSV GRCz10/danRer10
DCD009530DT: BEDGRAPH GRCz10/danRer10
DCD009531DT: BEDGRAPH GRCz10/danRer10
DCD009532DT: BEDGRAPH GRCz10/danRer10
DCD009533DT: BEDGRAPH GRCz10/danRer10
DCD009534DT: PDF GRCz10/danRer10
DCD009535DT: LOG GRCz10/danRer10
DCD009536DT: PDF GRCz10/danRer10
DCD009537DT: LOG GRCz10/danRer10
DCD009538DT: BAM GRCz10/danRer10
DCD015890DT: LOG GRCz11/danRer11
DCD015892DT: TSV GRCz11/danRer11
DCD015893DT: TSV GRCz11/danRer11
DCD015894DT: BEDGRAPH GRCz11/danRer11
DCD015895DT: BIGWIG GRCz11/danRer11
DCD015897DT: LOG GRCz11/danRer11
DCD015898DT: PDF GRCz11/danRer11
DCD015899DT: LOG GRCz11/danRer11
DCD015900DT: PDF GRCz11/danRer11
DCD015913DT: BEDGRAPH GRCz11/danRer11
DCD015921DT: BAM GRCz11/danRer11