Series Summary for DCD000309SR

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Survey

10.1186/s12864-015-2135-7

GSE57169

The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish, substantially less microRNAs have been discovered in zebrafish compared to human (miRBase Release 19). It appears that most of the miRNAs in zebrafish are yet to be discovered.We sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish. In brain, gut and liver sequencing was done sex specifically. Majority of the sequenced reads (16-62 %) mapped to known miRNAs, with the exception of ovary (5.7 %) and testis (7.8 %). Using the miRNA discovery tool (miRDeep2), we discovered novel miRNAs from the unannotated reads that ranged from 7.6 to 23.0 %, with exceptions of ovary (51.4 %) and testis (55.2 %). The prediction tool identified a total of 459 novel pre-miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated (22) and sex associated (34) miRNAs, respectively.This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further, we have discovered 459 novel pre-miRNAs (~30 % seed homology to human miRNA) as a genomic resource which can facilitate further investigations to understand miRNA-mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs.

True

mickael.dong

April 6, 2017, 1:50 a.m.

Sept. 27, 2017, 8:47 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006813BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD001671AA DCD013133BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001774SQ DCD001759TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004245DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001670AA DCD013134BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001773SQ DCD001758TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004244DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001669AA DCD013135BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001772SQ DCD001757TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004243DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006814BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD001668AA DCD013136BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001771SQ DCD001756TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004242DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001667AA DCD013137BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001770SQ DCD001755TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004241DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001666AA DCD013138BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001769SQ DCD001754TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004240DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006815BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD001665AA DCD013139BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001768SQ DCD001753TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004239DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001664AA DCD013140BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001767SQ DCD001752TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004238DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001663AA DCD013141BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001766SQ DCD001751TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004237DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006816BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD001662AA DCD013142BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001765SQ DCD001750TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004236DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001661AA DCD013143BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001764SQ DCD001749TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004235DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001660AA DCD013144BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001763SQ DCD001748TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004234DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006817BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD001659AA DCD013145BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001762SQ DCD001747TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004233DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001658AA DCD013146BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001761SQ DCD001746TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004232DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001657AA DCD013147BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001760SQ DCD001745TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004231DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006818BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD001656AA DCD013148BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001759SQ DCD001744TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004230DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001655AA DCD013149BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001758SQ DCD001743TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004229DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001654AA DCD013150BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001757SQ DCD001742TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004228DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006819BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD001653AA DCD013151BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001756SQ DCD001741TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004227DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001652AA DCD013152BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001755SQ DCD001740TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004226DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001651AA DCD013153BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001754SQ DCD001739TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004225DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006820BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD001650AA DCD013154BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001753SQ DCD001738TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004224DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001649AA DCD013155BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001752SQ DCD001737TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004223DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001648AA DCD013156BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001751SQ DCD001736TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004222DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006821BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD001647AA DCD013157BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001750SQ DCD001735TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004221DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001646AA DCD013158BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001749SQ DCD001734TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004220DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001645AA DCD013159BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001748SQ DCD001733TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004219DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006822BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD001644AA DCD013160BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001747SQ DCD001732TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004218DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001643AA DCD013161BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001746SQ DCD001731TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004217DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001642AA DCD013162BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001745SQ DCD001730TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004216DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006823BS DCD000309SR tissue Mathavan Lab, NTU Medical School SING 26+ somites 22
Applied Assay ID Biosample Replicate Assay
DCD001641AA DCD013163BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001744SQ DCD001729TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004215DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001640AA DCD013164BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001743SQ DCD001728TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004214DT: FASTQ
Applied Assay ID Biosample Replicate Assay
DCD001639AA DCD013165BR miRNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD001742SQ DCD001727TR Mathavan Lab, NTU Medical School Illumina HiSeq 2000 10/16/2015
DCD004213DT: FASTQ