{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_strategy = \"miRNA-Seq\" and tissue_curation_coarse = \"Reproductive System\"", "rows": [[15550, "ERR647595", "ERX604031", "ERS557915", "ERP007147", "PRJEB7420", "Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq", "ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622", "Other", "There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10\u2013300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.", null, null, null, "Egg", "SAMEA2796300", "UNIVERSITY OF AMSTERDAM", "Alias:Egg|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:29:23Z|INSDC status:public|SRA accession:ERS557915|Sample Name:ERS557915|Title:Zebrafish Egg samples|dev stage:Oocytes", null, null, null, null, null, null, null, null, "Ion Torrent Proton sequencing", "ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1", "RID0024", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "ERP007147", "Ion Torrent Proton sequencing", "ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16", "RID0024_016.fastq.gz", "fastq", 6684767188.0, 89052017.0, "ena RUN UNIVERSITY OF 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Testis2", "ZF2Testis2", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "1010Application ReadForward1", "SRP039502", null, null, "ZF2_Testis_3.fq.gz", "fastq", 1192024422.0, 11802222.0, "Testis2 Run3", "0:101", "A:373380865;C:276125943;G:251033102;T:290931637;N:552875", 101, null, null, null, 373380865, 276125943, 251033102, 290931637, 552875, "SRX685395", "SRS686644", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 3e-05, null, 1e-05, null, 0.99997, null, 0.0, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Gonad", "Reproductive System"], [37925, "SRR1554483", "SRX685391", "SRS686559", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF3Ovary1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Ovary1", "ZF3Ovary2", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "1010Application ReadForward1", "SRP039502", null, null, "ZF3_Ovary_3.fq.gz", "fastq", 347516154.0, 3440754.0, "Ovary1 Run3", "0:101", "A:107805981;C:80183725;G:73617313;T:85763181;N:145954", 101, null, null, null, 107805981, 80183725, 73617313, 85763181, 145954, "SRX685391", "SRS686559", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 5e-05, null, 4e-05, null, 1.0, null, null, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Gonad", "Reproductive System"], [37926, "SRR1554480", "SRX685390", "SRS686542", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain 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"A:340636900;C:278505979;G:259975802;T:304564724;N:545231", 101, null, null, null, 340636900, 278505979, 259975802, 304564724, 545231, "SRX685390", "SRS686542", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 1e-05, null, 0.0, null, 1.0, null, null, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Gonad", "Reproductive System"], [37929, "SRR1554493", "SRX683354", "SRS686645", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF4Ovary1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Ovary2", "ZF4Ovary1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "510Application ReadForward1", "SRP039502", null, null, "ZF4_Ovary_1.fq.gz", "fastq", 476104278.0, 9335378.0, "Ovary2 Run1", "0:51", "A:111060704;C:120863975;G:129849761;T:114224677;N:105161", 51, null, null, null, 111060704, 120863975, 129849761, 114224677, 105161, "SRX683354", "SRS686645", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 0.00027, null, 8e-05, null, 0.99945, null, 0.8125, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Gonad", "Reproductive System"], [37930, "SRR1554494", "SRX683354", "SRS686645", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF4Ovary1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97410|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Ovary2", "ZF4Ovary1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "510Application ReadForward1", "SRP039502", null, null, "ZF4_Ovary_2.fq.gz", "fastq", 561956352.0, 11018752.0, "Ovary2 Run2", "0:51", "A:129925815;C:148479658;G:148478706;T:132824290;N:2247883", 51, null, null, null, 129925815, 148479658, 148478706, 132824290, 2247883, "SRX683354", "SRS686645", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 0.00022, null, 0.0001, null, 0.99967, null, 0.6875, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Gonad", "Reproductive System"], [37931, "SRR1554490", "SRX683353", "SRS686644", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF2Testis1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Testis2", "ZF2Testis1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "510Application ReadForward1", "SRP039502", null, null, "ZF2_Testis_1.fq.gz", "fastq", 586152231.0, 11493181.0, "Testis2 Run1", "0:51", "A:145360493;C:148943988;G:151402108;T:140286245;N:159397", 51, null, null, null, 145360493, 148943988, 151402108, 140286245, 159397, "SRX683353", "SRS686644", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 8e-05, null, 2e-05, null, 0.99985, null, 0.57142, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Gonad", "Reproductive System"], [37932, "SRR1554491", "SRX683353", "SRS686644", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF2Testis1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97409|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Testis2", "ZF2Testis1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "510Application ReadForward1", "SRP039502", null, null, "ZF2_Testis_2.fq.gz", "fastq", 697016337.0, 13666987.0, "Testis2 Run2", "0:51", 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97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Ovary1", "ZF3Ovary1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "510Application ReadForward1", "SRP039502", null, null, "ZF3_Ovary_1.fq.gz", "fastq", 116086965.0, 2276215.0, "Ovary1 Run1", "0:51", "A:29237121;C:30235277;G:29264328;T:27320814;N:29425", 51, null, null, null, 29237121, 30235277, 29264328, 27320814, 29425, "SRX683080", "SRS686559", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 0.00022, null, 9e-05, null, 0.99967, null, 0.65, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Gonad", "Reproductive System"], [37938, "SRR1554482", "SRX683080", "SRS686559", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF3Ovary1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97406|sex:female|tissue:Ovary|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Ovary1", "ZF3Ovary1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "510Application ReadForward1", "SRP039502", null, null, "ZF3_Ovary_2.fq.gz", "fastq", 138905844.0, 2723644.0, "Ovary1 Run2", "0:51", "A:34695180;C:38015933;G:33434207;T:32057083;N:703441", 51, null, null, null, 34695180, 38015933, 33434207, 32057083, 703441, "SRX683080", "SRS686559", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 0.00016, null, 5e-05, null, 0.99977, null, 0.42857, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Gonad", "Reproductive System"], [37939, "SRR1554478", "SRX683062", "SRS686542", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF1Testis1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Testis1", "ZF1Testis1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "510Application ReadForward1", "SRP039502", null, null, "ZF1_Testis_1.fq.gz", "fastq", 655515750.0, 12853250.0, "Testis1 Run1", "0:51", "A:152422885;C:163771947;G:179144090;T:159997538;N:179290", 51, null, null, null, 152422885, 163771947, 179144090, 159997538, 179290, "SRX683062", "SRS686542", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 0.0011, null, 0.00053, null, 0.99829, null, 0.67777, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Gonad", "Reproductive System"], [37940, "SRR1554479", "SRX683062", "SRS686542", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF1Testis1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97405|sex:male|tissue:Testis|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Testis1", "ZF1Testis1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "510Application ReadForward1", "SRP039502", null, null, "ZF1_Testis_2.fq.gz", "fastq", 777594399.0, 15246949.0, "Testis1 Run2", "0:51", "A:180116528;C:202508153;G:204833105;T:186435696;N:3700917", 51, null, null, null, 180116528, 202508153, 204833105, 186435696, 3700917, "SRX683062", "SRS686542", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 0.00073, null, 0.00032, null, 0.99898, null, 0.62745, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Gonad", "Reproductive System"], [37997, "SRR1265760", "SRX529154", "SRS598851", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "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 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 in male and female separately. 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 un annotated 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. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Testis Replicate 3 sRNAseq", "GSM1376643", null, "source name:Testis|gender:male|tissue:Testis|genetic background:Wild type Singapore strain", "Testis Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Testis", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Testis|genetic background:Wild type Singapore strain", "GSM1376643", "GSM1376643: Testis Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376643", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376643", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZT004_GCCAAT_L004_R1.fastq.gz", "fastq", 1096387628.0, 14426153.0, "GSM1376643 r1", "0:76", "A:268706118;C:286539627;G:262643519;T:278353167;N:145197", 76, null, null, null, 268706118, 286539627, 262643519, 278353167, 145197, "SRX529154", "SRS598851", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00659, null, 0.00333, null, 0.99845, null, 0.7331, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [37998, "SRR1265759", "SRX529153", "SRS598850", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "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 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 in male and female separately. 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 un annotated 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. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Testis Replicate 2 sRNAseq", "GSM1376642", null, "source name:Testis|gender:male|tissue:Testis|genetic background:Wild type Singapore strain", "Testis Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Testis", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Testis|genetic background:Wild type Singapore strain", "GSM1376642", "GSM1376642: Testis Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376642", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376642", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZT003_ACAGTG_L004_R1.fastq.gz", "fastq", 1562745896.0, 20562446.0, "GSM1376642 r1", "0:76", "A:381752411;C:387452090;G:395892335;T:397438930;N:210130", 76, null, null, null, 381752411, 387452090, 395892335, 397438930, 210130, "SRX529153", "SRS598850", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.01222, null, 0.00651, null, 0.99788, null, 0.69591, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [37999, "SRR1265758", "SRX529152", "SRS598849", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "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 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 in male and female separately. 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 un annotated 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. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Testis Replicate 1 sRNAseq", "GSM1376641", null, "source name:Testis|gender:male|tissue:Testis|genetic background:Wild type Singapore strain", "Testis Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Testis", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Male|tissue:Testis|genetic background:Wild type Singapore strain", "GSM1376641", "GSM1376641: Testis Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376641", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376641", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZT001_TGACCA_L004_R1.fastq.gz", "fastq", 1368892316.0, 18011741.0, "GSM1376641 r1", "0:76", "A:335715713;C:358829703;G:326742789;T:347419137;N:184974", 76, null, null, null, 335715713, 358829703, 326742789, 347419137, 184974, "SRX529152", "SRS598849", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00032, null, 3e-05, null, 0.99943, null, 0.69387, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [38000, "SRR1265757", "SRX529151", "SRS598848", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "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 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 in male and female separately. 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 un annotated 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. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Ovary Replicate 3 sRNAseq", "GSM1376640", null, "source name:Ovary|gender:female|tissue:Ovary|genetic background:Wild type Singapore strain", "Ovary Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Ovary", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Ovary|genetic background:Wild type Singapore strain", "GSM1376640", "GSM1376640: Ovary Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376640", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376640", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZO006_GATCAG_L008_R1.fastq.gz", "fastq", 1411005984.0, 27666784.0, "GSM1376640 r1", "0:51", "A:326542153;C:314421825;G:411019622;T:358847379;N:175005", 51, null, null, null, 326542153, 314421825, 411019622, 358847379, 175005, "SRX529151", "SRS598848", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00638, null, 0.00068, null, 0.99513, null, 0.75483, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [38001, "SRR1265756", "SRX529150", "SRS598847", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "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 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 in male and female separately. 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 un annotated 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. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Ovary Replicate 2 sRNAseq", "GSM1376639", null, "source name:Ovary|gender:female|tissue:Ovary|genetic background:Wild type Singapore strain", "Ovary Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Ovary", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Ovary|genetic background:Wild type Singapore strain", "GSM1376639", "GSM1376639: Ovary Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376639", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376639", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZO005_ACTTGA_L008_R1.fastq.gz", "fastq", 765419424.0, 15008224.0, "GSM1376639 r1", "0:51", "A:179455664;C:170237021;G:221342071;T:194287721;N:96947", 51, null, null, null, 179455664, 170237021, 221342071, 194287721, 96947, "SRX529150", "SRS598847", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.02512, null, 0.00355, null, 0.98212, null, 0.67744, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [38002, "SRR1265755", "SRX529149", "SRS598846", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "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 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 in male and female separately. 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 un annotated 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. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Ovary Replicate 1 sRNAseq", "GSM1376638", null, "source name:Ovary|gender:female|tissue:Ovary|genetic background:Wild type Singapore strain", "Ovary Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p m r t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Ovary", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "gender:Female|tissue:Ovary|genetic background:Wild type Singapore strain", "GSM1376638", "GSM1376638: Ovary Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376638", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376638", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZO004_CAGATC_L008_R1.fastq.gz", "fastq", 487558674.0, 9559974.0, "GSM1376638 r1", "0:51", "A:114833813;C:108951811;G:140408702;T:123302557;N:61791", 51, null, null, null, 114833813, 108951811, 140408702, 123302557, 61791, "SRX529149", "SRS598846", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00298, null, 0.0004, null, 0.99644, null, 0.84584, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Gonad", "Reproductive System"], [38256, "SRR1596061", "SRX719267", "SRS715451", "SRP048591", "PRJNA262865", "Identification and Characterization of MicroRNAs in Zebrafish Spermatozoa by Illumina Sequencing", "GSE61984", "Other", "MicroRNAs miRNAs are involved in nearly every biological process examined to date. Mounting evidence show that some spermatozoa specific miRNAs play important roles in the regulation of spermatogenesis and germ cells development but little is known of the exact identity and function of miRNA in sperm cells or their potential involvement in spermatogenesis and germ cells development. Here we investigated the spermatozoa miRNA profiles using illumina deep sequencing combined with bioinformatic analysis using zebrafish as a model system. Deep sequencing of small RNAs yielded 12 million raw reads from zebrafish spermatozoa. Analysis showed that the noncoding RNA of the spermatozoa included tRNA rRNA snRNA snoRNA and miRNA. By mapping to the zebrafish genome we identified 400 novel and 204 conserved miRNAs which could be grouped into 104 families including zebrafish specific families such as mir 731 mir 724 mir 725 mir 729 and mir 2185. We report the first characterization of the miRNAs profiling in zebrafish spermatozoa. The obtained spermatozoa miRNAs profiling will serve as valuable resources to systematically study spermatogenesis in fish and vertebrate. Overall design: Examination of small RNA populations in zebrafish spermatozoa", null, "pubmed:26418264", null, "zebrafish sperm", "GSM1517943", null, "tissue:Zebrafish Spermatozoa|cell type:Spermatozoa|strain:AB wild type", "zebrafish sperm", "The sequencing data were analyzed as described previously by Xu et al 2014. The low quality reads were filtered to remove reads without xxx 3\u2019 adaptor 5\u2019 adaptor contaminant reads reads without xxx insert fragment reads containing polyA stretches and reads of less than 18 nt. Next the remaining sequences clean reads were mapped to the zebrafish genome using SOAP with a tolerance of one mismatch to analyze their distribution The sequences were aligned against known miRNA precursors and mature miRNAs deposited in the miRBase 20.0 to identify conserved miRNAs. The clean reads were compared against the sRNAs rRNAs tRNAs snRNAs snoRNA miRNA deposited in the GenBank and Rfam http://www.sanger.ac.uk/resources/databases/rfam.html databases to annotate the sRNA sequences. Because some sRNA tags might map to more than one category we used priority rules to ensure that every unique sRNA was mapped to only one annotation as follows: rRNA etc. GenBank >Rfam >known miRNA >repeat >exon >intron. Genome build: miRBase 20.0 Supplementary files format and content: zebrafish miRNA count.txt include RPKM values of each known miRNA in this sample", "Zebrafish Spermatozoa", null, "Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer\u2019s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer Agilent Technologies. RNA samples that passed the quality check were sent to BGI Shenzhen China for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform.", null, "cell type:Spermatozoa|strain:AB wild type", "GSM1517943", "GSM1517943: zebrafish sperm; Danio rerio; miRNA Seq", "GSM1517943", null, "1", "Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer\u2019s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer Agilent Technologies. RNA samples that passed the quality check were sent to BGI Shenzhen China for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform.", "GEO Accession:GSM1517943", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048591", null, null, "zebrafish-sperm5.fq.bz2", "fastq", 588000000.0, 12000000.0, "GSM1517943 r1", "0:49", "A:122673394;C:136175879;G:140377184;T:188702650;N:70893", 49, null, null, null, 122673394, 136175879, 140377184, 188702650, 70893, "SRX719267", "SRS715451", "SRA188511", "GEO", "SUN YAT-SEN UNIVERSITY", 1, 2e-05, null, 0.0, null, 0.99997, null, 1.0, null, 49, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2014-10-02", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [52326, "SRR9119512", "SRX5893495", "SRS4815090", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIb 3", "GSM3816534", null, "source name:stage IIIb follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "IIIb 3", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIb follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "GSM3816534", "GSM3816534: IIIb 3; Danio rerio; miRNA Seq", "GSM3816534", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816534", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.005.RPI10.IIIb_3_R1.fastq.gz", "fastq", 1449340900.0, 28986818.0, "GSM3816534 r1", "0:50 1:0", "A:351029701;C:324452324;G:401722902;T:371889768;N:246205", 50, 0, null, null, 351029701, 324452324, 401722902, 371889768, 246205, "SRX5893495", "SRS4815090", "SRA890399", "GEO", "Biology, YorkU", 1, 0.08662, null, 0.01333, null, 0.96213, null, 0.83838, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52327, "SRR9119513", "SRX5893495", "SRS4815090", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIb 3", "GSM3816534", null, "source name:stage IIIb follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "IIIb 3", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIb follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "GSM3816534", "GSM3816534: IIIb 3; Danio rerio; miRNA Seq", "GSM3816534", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816534", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.006.RPI10.IIIb_3_R1.fastq", "fastq", 1447621100.0, 28952422.0, "GSM3816534 r2", "0:50 1:0", "A:350650304;C:324162528;G:401055729;T:371582418;N:170121", 50, 0, null, null, 350650304, 324162528, 401055729, 371582418, 170121, "SRX5893495", "SRS4815090", "SRA890399", "GEO", "Biology, YorkU", 1, 0.08676, null, 0.01312, null, 0.96282, null, 0.84604, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52328, "SRR9119510", "SRX5893494", "SRS4815089", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIb 2", "GSM3816533", null, "source name:stage IIIb follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "IIIb 2", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIb follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "GSM3816533", "GSM3816533: IIIb 2; Danio rerio; miRNA Seq", "GSM3816533", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816533", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.005.RPI9.IIIb_2_R1.fastq.gz", "fastq", 1012538750.0, 20250775.0, "GSM3816533 r1", "0:50 1:0", "A:242873339;C:228078637;G:287889366;T:253526026;N:171382", 50, 0, null, null, 242873339, 228078637, 287889366, 253526026, 171382, "SRX5893494", "SRS4815089", "SRA890399", "GEO", "Biology, YorkU", 1, 0.04745, null, 0.00802, null, 0.968, null, 0.75298, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52329, "SRR9119511", "SRX5893494", "SRS4815089", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIb 2", "GSM3816533", null, "source name:stage IIIb follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "IIIb 2", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIb follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "GSM3816533", "GSM3816533: IIIb 2; Danio rerio; miRNA Seq", "GSM3816533", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816533", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.006.RPI9.IIIb_2_R1.fastq", "fastq", 1010559400.0, 20211188.0, "GSM3816533 r2", "0:50 1:0", "A:242471282;C:227664296;G:287157957;T:253147388;N:118477", 50, 0, null, null, 242471282, 227664296, 287157957, 253147388, 118477, "SRX5893494", "SRS4815089", "SRA890399", "GEO", "Biology, YorkU", 1, 0.04679, null, 0.008, null, 0.96946, null, 0.71268, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52330, "SRR9119508", "SRX5893493", "SRS4815088", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIb 1", "GSM3816532", null, "source name:stage IIIb follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "IIIb 1", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIb follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "GSM3816532", "GSM3816532: IIIb 1; Danio rerio; miRNA Seq", "GSM3816532", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816532", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.005.RPI8.IIIb_1_R1.fastq.gz", "fastq", 1443846950.0, 28876939.0, "GSM3816532 r1", "0:50 1:0", "A:350805103;C:319766230;G:407583206;T:365448522;N:243889", 50, 0, null, null, 350805103, 319766230, 407583206, 365448522, 243889, "SRX5893493", "SRS4815088", "SRA890399", "GEO", "Biology, YorkU", 1, 0.02559, null, 0.00389, null, 0.98407, null, 0.82023, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52331, "SRR9119509", "SRX5893493", "SRS4815088", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIb 1", "GSM3816532", null, "source name:stage IIIb follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "IIIb 1", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIb follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIb", "GSM3816532", "GSM3816532: IIIb 1; Danio rerio; miRNA Seq", "GSM3816532", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816532", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.006.RPI8.IIIb_1_R1.fastq", "fastq", 1442694250.0, 28853885.0, "GSM3816532 r2", "0:50 1:0", "A:350607715;C:319569609;G:407049947;T:365297986;N:168993", 50, 0, null, null, 350607715, 319569609, 407049947, 365297986, 168993, "SRX5893493", "SRS4815088", "SRA890399", "GEO", "Biology, YorkU", 1, 0.02565, null, 0.00409, null, 0.98417, null, 0.81633, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52332, "SRR9119506", "SRX5893492", "SRS4815087", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIa 3", "GSM3816531", null, "source name:stage IIIa follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "IIIa 3", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIa follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "GSM3816531", "GSM3816531: IIIa 3; Danio rerio; miRNA Seq", "GSM3816531", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816531", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.005.RPI4.IIIa_3_R1.fastq.gz", "fastq", 1324489100.0, 26489782.0, "GSM3816531 r1", "0:50 1:0", "A:333465386;C:289207984;G:364882545;T:336711699;N:221486", 50, 0, null, null, 333465386, 289207984, 364882545, 336711699, 221486, "SRX5893492", "SRS4815087", "SRA890399", "GEO", "Biology, YorkU", 1, 0.02703, null, 0.00432, null, 0.98313, null, 0.75385, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52333, "SRR9119507", "SRX5893492", "SRS4815087", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIa 3", "GSM3816531", null, "source name:stage IIIa follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "IIIa 3", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIa follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "GSM3816531", "GSM3816531: IIIa 3; Danio rerio; miRNA Seq", "GSM3816531", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816531", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.006.RPI4.IIIa_3_R1.fastq", "fastq", 1322554650.0, 26451093.0, "GSM3816531 r2", "0:50 1:0", "A:333031673;C:288843797;G:364209143;T:336315522;N:154515", 50, 0, null, null, 333031673, 288843797, 364209143, 336315522, 154515, "SRX5893492", "SRS4815087", "SRA890399", "GEO", "Biology, YorkU", 1, 0.02671, null, 0.00422, null, 0.98283, null, 0.76748, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52334, "SRR9119504", "SRX5893491", "SRS4815086", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIa 2", "GSM3816530", null, "source name:stage IIIa follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "IIIa 2", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIa follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "GSM3816530", "GSM3816530: IIIa 2; Danio rerio; miRNA Seq", "GSM3816530", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816530", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.005.RPI3.IIIa_2_R1.fastq.gz", "fastq", 1382308600.0, 27646172.0, "GSM3816530 r1", "0:50 1:0", "A:342206537;C:301597185;G:385756857;T:352517232;N:230789", 50, 0, null, null, 342206537, 301597185, 385756857, 352517232, 230789, "SRX5893491", "SRS4815086", "SRA890399", "GEO", "Biology, YorkU", 1, 0.05315, null, 0.00892, null, 0.9643, null, 0.79967, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52335, "SRR9119505", "SRX5893491", "SRS4815086", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIa 2", "GSM3816530", null, "source name:stage IIIa follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "IIIa 2", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIa follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "GSM3816530", "GSM3816530: IIIa 2; Danio rerio; miRNA Seq", "GSM3816530", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816530", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.006.RPI3.IIIa_2_R1.fastq", "fastq", 1383050750.0, 27661015.0, "GSM3816530 r2", "0:50 1:0", "A:342441286;C:301828080;G:385820344;T:352800933;N:160107", 50, 0, null, null, 342441286, 301828080, 385820344, 352800933, 160107, "SRX5893491", "SRS4815086", "SRA890399", "GEO", "Biology, YorkU", 1, 0.0533, null, 0.00892, null, 0.96323, null, 0.81292, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52336, "SRR9119502", "SRX5893490", "SRS4815085", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIa 1", "GSM3816529", null, "source name:stage IIIa follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "IIIa 1", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIa follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "GSM3816529", "GSM3816529: IIIa 1; Danio rerio; miRNA Seq", "GSM3816529", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816529", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.005.RPI2.IIIa_1_R1.fastq.gz", "fastq", 1333818450.0, 26676369.0, "GSM3816529 r1", "0:50 1:0", "A:320039883;C:296663387;G:380656068;T:336233800;N:225312", 50, 0, null, null, 320039883, 296663387, 380656068, 336233800, 225312, "SRX5893490", "SRS4815085", "SRA890399", "GEO", "Biology, YorkU", 1, 0.0976, null, 0.019, null, 0.93718, null, 0.75404, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [52337, "SRR9119503", "SRX5893490", "SRS4815085", "SRP199448", "PRJNA544696", "Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells", "GSE131759", "Transcriptome Analysis", "MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expression profiles in somatic cells within the zebrafish ovarian follicles. The differential expression of miRNAs between stage IIIa and IIIb follicular cells suggests that these miRNAs are important regulators of zebrafish ovarian follicle development and/or oocyte maturation. Overall design: miRNA seq analysis in stage IIIa and IIIb vitellogenic zebrafish follicular cells.", null, "pubmed:31417497", null, "IIIa 1", "GSM3816529", null, "source name:stage IIIa follicular cells|tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "IIIa 1", "LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample", "stage IIIa follicular cells", null, "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:ovary|cell type:follicular cells|developmental stage:IIIa", "GSM3816529", "GSM3816529: IIIa 1; Danio rerio; miRNA Seq", "GSM3816529", null, "1", "Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3816529", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP199448", null, null, "HI.2030.006.RPI2.IIIa_1_R1.fastq", "fastq", 1334152750.0, 26683055.0, "GSM3816529 r2", "0:50 1:0", "A:320194547;C:296827909;G:380547854;T:336424243;N:158197", 50, 0, null, null, 320194547, 296827909, 380547854, 336424243, 158197, "SRX5893490", "SRS4815085", "SRA890399", "GEO", "Biology, YorkU", 1, 0.09727, null, 0.01947, null, 0.93866, null, 0.76527, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2019-05-24", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [60887, "SRR12628234", "SRX9110497", "SRS7353480", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs", null, "pubmed:33506864", null, "h24 2: PGCs 24hpf repeat2", "GSM4777194", null, "source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad", "h24 2: PGCs 24hpf repeat2", "Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample \u2026", "PGCs", null, "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", null, "cell type:primordial germ cells|strain:AB|tissue:gonad", "GSM4777194", "GSM4777194: h24 2: PGCs 24hpf repeat2; Danio rerio; miRNA Seq", "GSM4777194", null, "1", "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", "GEO Accession:GSM4777194", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP282187", null, null, "h24_2.fastq", "fastq", 4024398750.0, 26829325.0, "GSM4777194 r1", "0:150 1:0", "A:1030703487;C:1025857271;G:1004392553;T:963376583;N:68856", 150, 0, null, null, 1030703487, 1025857271, 1004392553, 963376583, 68856, "SRX9110497", "SRS7353480", "SRA1124474", "GEO", "Shanghai Institute of Biochemistry and Cell Biology,CAS", 1, 0.00025, null, 0.0, null, 0.99997, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-12", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [60888, "SRR12628233", "SRX9110496", "SRS7353479", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs", null, "pubmed:33506864", null, "h24 1: PGCs 24hpf repeat1", "GSM4777193", null, "source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad", "h24 1: PGCs 24hpf repeat1", "Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample \u2026", "PGCs", null, "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", null, "cell type:primordial germ cells|strain:AB|tissue:gonad", "GSM4777193", "GSM4777193: h24 1: PGCs 24hpf repeat1; Danio rerio; miRNA Seq", "GSM4777193", null, "1", "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", "GEO Accession:GSM4777193", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP282187", null, null, "h24_1.fastq", "fastq", 2223111450.0, 14820743.0, "GSM4777193 r1", "0:150 1:0", "A:510125618;C:561938103;G:577742482;T:573267493;N:37754", 150, 0, null, null, 510125618, 561938103, 577742482, 573267493, 37754, "SRX9110496", "SRS7353479", "SRA1124474", "GEO", "Shanghai Institute of Biochemistry and Cell Biology,CAS", 1, 0.0004, null, 0.0, null, 0.99993, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-12", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [60889, "SRR12628232", "SRX9110495", "SRS7353478", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs", null, "pubmed:33506864", null, "h11 2: PGCs 11hpf repeat2", "GSM4777192", null, "source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad", "h11 2: PGCs 11hpf repeat2", "Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample \u2026", "PGCs", null, "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", null, "cell type:primordial germ cells|strain:AB|tissue:gonad", "GSM4777192", "GSM4777192: h11 2: PGCs 11hpf repeat2; Danio rerio; miRNA Seq", "GSM4777192", null, "1", "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", "GEO Accession:GSM4777192", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP282187", null, null, "h11_2.fastq", "fastq", 1725506100.0, 11503374.0, "GSM4777192 r1", "0:150 1:0", "A:419294958;C:415643261;G:432730446;T:457808038;N:29397", 150, 0, null, null, 419294958, 415643261, 432730446, 457808038, 29397, "SRX9110495", "SRS7353478", "SRA1124474", "GEO", "Shanghai Institute of Biochemistry and Cell Biology,CAS", 1, 0.00062, null, 0.0, null, 0.99991, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-12", "Segmentation", "Embryo", "Gonad", "Reproductive System"], [60890, "SRR12628231", "SRX9110494", "SRS7353477", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs", null, "pubmed:33506864", null, "h11 1: PGCs 11hpf repeat1", "GSM4777191", null, "source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad", "h11 1: PGCs 11hpf repeat1", "Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample \u2026", "PGCs", null, "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", null, "cell type:primordial germ cells|strain:AB|tissue:gonad", "GSM4777191", "GSM4777191: h11 1: PGCs 11hpf repeat1; Danio rerio; miRNA Seq", "GSM4777191", null, "1", "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", "GEO Accession:GSM4777191", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP282187", null, null, "h11_1.fastq", "fastq", 2690366550.0, 17935777.0, "GSM4777191 r1", "0:150 1:0", "A:722881530;C:687611993;G:633563837;T:646263376;N:45814", 150, 0, null, null, 722881530, 687611993, 633563837, 646263376, 45814, "SRX9110494", "SRS7353477", "SRA1124474", "GEO", "Shanghai Institute of Biochemistry and Cell Biology,CAS", 1, 0.0006, null, 0.0, null, 0.99991, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-12", "Segmentation", "Embryo", "Gonad", "Reproductive System"], [60891, "SRR12628230", "SRX9110493", "SRS7353476", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs", null, "pubmed:33506864", null, "h6 2: PGCs 6hpf repeat2", "GSM4777190", null, "source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad", "h6 2: PGCs 6hpf repeat2", "Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample \u2026", "PGCs", null, "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", null, "cell type:primordial germ cells|strain:AB|tissue:gonad", "GSM4777190", "GSM4777190: h6 2: PGCs 6hpf repeat2; Danio rerio; miRNA Seq", "GSM4777190", null, "1", "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", "GEO Accession:GSM4777190", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP282187", null, null, "h6_2.fastq", "fastq", 2330922150.0, 15539481.0, "GSM4777190 r1", "0:150 1:0", "A:563758043;C:619336180;G:552040747;T:595747277;N:39903", 150, 0, null, null, 563758043, 619336180, 552040747, 595747277, 39903, "SRX9110493", "SRS7353476", "SRA1124474", "GEO", "Shanghai Institute of Biochemistry and Cell Biology,CAS", 1, 0.00014, null, 0.0, null, 0.99997, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-12", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [60892, "SRR12628229", "SRX9110492", "SRS7353475", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs", null, "pubmed:33506864", null, "h6 1: PGCs 6hpf repeat1", "GSM4777189", null, "source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad", "h6 1: PGCs 6hpf repeat1", "Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample \u2026", "PGCs", null, "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", null, "cell type:primordial germ cells|strain:AB|tissue:gonad", "GSM4777189", "GSM4777189: h6 1: PGCs 6hpf repeat1; Danio rerio; miRNA Seq", "GSM4777189", null, "1", "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", "GEO Accession:GSM4777189", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP282187", null, null, "h6_1.fastq", "fastq", 1979588400.0, 13197256.0, "GSM4777189 r1", "0:150 1:0", "A:453046525;C:471873747;G:495904656;T:558729697;N:33775", 150, 0, null, null, 453046525, 471873747, 495904656, 558729697, 33775, "SRX9110492", "SRS7353475", "SRA1124474", "GEO", "Shanghai Institute of Biochemistry and Cell Biology,CAS", 1, 0.00028, null, 0.0, null, 0.99997, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-12", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [64249, "SRR14373546", "SRX10725858", "SRS8815710", "SRP318063", "PRJNA726592", 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Library was constructed using sequencing Lane 1x50 v4 HiSeq single end mode with a read length of 50 bp", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP332839", null, null, "ZF_36_G15_22313_TCATTC.fastq", "fastq", 1465003700.0, 29300074.0, "ZF 36 G15 22313 TCATTC.fastq", "0:50 1:0", "A:431488151;C:331693370;G:386155519;T:315491607;N:175053", 50, 0, null, null, 431488151, 331693370, 386155519, 315491607, 175053, "SRX11797840", "SRS9797775", "SRA1279325", "Institute of Marine Sciences|Repro-Immune Team", "Institute of Marine Sciences", 1, 0.72513, null, 0.40489, null, 0.86229, null, 0.50704, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2021-08-17", "Adult", "Adult", "Gonad", "Reproductive System"], [65683, "SRR15498152", "SRX11797839", "SRS9797774", "SRP332839", "PRJNA755482", "miRNA sequencing from zebrafish testes and ovaries exposed to normal and high temperatures", "PRJNA755482", "Other", "We exposed zebrafish to elevated temperatures during early development a treatment that is known to result in male skewed sex ratios in order to understand the role of the epigenetic regulation mediated by miRNAs in the gonads.", null, null, null, "Testis High Temperature", "ZF 36 G14M", null, "strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate THT 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of Danio rerio: adult treated testis", "36 G14", "36 G14", "NEBNext Small RNA Library Prep Set for Illumina was used on total RNA isolated from zebrafish testis using Qiagen RNeasy mini kit. Library was constructed using sequencing Lane 1x50 v4 HiSeq single end mode with a read length of 50 bp", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP332839", null, null, "ZF_36_G14_22313_CACGAT.fastq ZF_36_G14_24794_CACGAT.fastq", "fastq fastq", 454229750.0, 9084595.0, "ZF 36 G14 22313 CACGAT.fastq", "0:50 1:0", "A:133880771;C:103643537;G:119108795;T:97573024;N:23623", 50, 0, null, null, 133880771, 103643537, 119108795, 97573024, 23623, "SRX11797839", "SRS9797774", "SRA1279325", "Institute of Marine Sciences|Repro-Immune Team", "Institute of Marine Sciences", 1, 0.67716, null, 0.38799, null, 0.81949, null, 0.53484, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2021-08-17", "Adult", "Adult", "Gonad", "Reproductive System"], [65684, "SRR15498153", "SRX11797838", "SRS9797773", "SRP332839", "PRJNA755482", "miRNA sequencing from zebrafish testes and ovaries exposed to normal and high temperatures", "PRJNA755482", "Other", "We exposed zebrafish to elevated temperatures during early development a treatment that is known to result in male skewed sex ratios in order to understand the role of the epigenetic regulation mediated by miRNAs in the gonads.", null, null, null, "Testis High Temperature", "ZF 36 G11M", null, "strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate THT 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of Danio rerio: adult treated testis", "36 G11", "36 G11", "NEBNext Small RNA Library Prep Set for Illumina was used on total RNA isolated from zebrafish testis using Qiagen RNeasy mini kit. Library was constructed using sequencing Lane 1x50 v4 HiSeq single end mode with a read length of 50 bp", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP332839", null, null, "ZF_36_G11_22313_CAAAAG.fastq", "fastq", 309077000.0, 6181540.0, "ZF 36 G11 22313 CAAAAG.fastq", "0:50 1:0", "A:92340462;C:68123395;G:79403422;T:69172711;N:37010", 50, 0, null, null, 92340462, 68123395, 79403422, 69172711, 37010, "SRX11797838", "SRS9797773", "SRA1279325", "Institute of Marine Sciences|Repro-Immune Team", "Institute of Marine Sciences", 1, 0.68141, null, 0.45311, null, 0.86519, null, 0.52771, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2021-08-17", "Adult", "Adult", "Gonad", "Reproductive System"], [65685, "SRR15498154", "SRX11797837", "SRS9797772", "SRP332839", "PRJNA755482", "miRNA sequencing from zebrafish testes and ovaries exposed to normal and high temperatures", "PRJNA755482", "Other", "We exposed zebrafish to elevated temperatures during early development a treatment that is known to result in male skewed sex ratios in order to understand the role of the epigenetic regulation mediated by miRNAs in the gonads.", null, null, null, "Testis High Temperature", "ZF 36 G13M", null, "strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate THT 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of Danio rerio: adult treated testis", "36 G13", "36 G13", "NEBNext Small RNA Library Prep Set for Illumina was used on total RNA isolated from zebrafish testis using Qiagen RNeasy mini kit. Library was constructed using sequencing Lane 1x50 v4 HiSeq single end mode with a read length of 50 bp", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP332839", null, null, "ZF_36_G13_22969_TCGGCA.fastq", "fastq", 525673800.0, 10513476.0, "ZF 36 G13 22969 TCGGCA.fastq", "0:50 1:0", "A:154723201;C:115780155;G:137702409;T:117453866;N:14169", 50, 0, null, null, 154723201, 115780155, 137702409, 117453866, 14169, "SRX11797837", "SRS9797772", "SRA1279325", "Institute of Marine Sciences|Repro-Immune Team", "Institute of Marine Sciences", 1, 0.74813, null, 0.46889, null, 0.85299, null, 0.51699, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2021-08-17", "Adult", "Adult", "Gonad", "Reproductive System"], [65686, "SRR15498155", "SRX11797836", "SRS9797771", "SRP332839", "PRJNA755482", "miRNA sequencing from zebrafish testes and ovaries exposed to normal and high temperatures", "PRJNA755482", "Other", "We exposed zebrafish to elevated temperatures during early development a treatment that is known to result in male skewed sex ratios in order to understand the role of the epigenetic regulation mediated by miRNAs in the gonads.", null, null, null, "Ovary High Temperature", "ZF 36 G8F", null, "strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OHT 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of Danio rerio: adult treated ovary", "36 G8", "36 G8", "NEBNext Small RNA Library Prep Set for Illumina was used on total RNA isolated from zebrafish ovary using Qiagen RNeasy mini kit. Library was constructed using sequencing Lane 1x50 v4 HiSeq single end mode with a read length of 50 bp", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP332839", null, null, "ZF_36_G8_22313_GTGAAA.fastq ZF_36_G8_24794_GTGAAA.fastq", "fastq fastq", 354863200.0, 7097264.0, "ZF 36 G8 22313 GTGAAA.fastq", "0:50 1:0", "A:106167879;C:78499963;G:93422866;T:76761338;N:11154", 50, 0, null, null, 106167879, 78499963, 93422866, 76761338, 11154, "SRX11797836", "SRS9797771", "SRA1279325", "Institute of Marine Sciences|Repro-Immune Team", "Institute of Marine Sciences", 1, 0.74342, null, 0.50048, null, 0.82919, null, 0.51092, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2021-08-17", "Adult", "Adult", "Gonad", "Reproductive System"], [65687, "SRR15498156", "SRX11797835", "SRS9797770", "SRP332839", "PRJNA755482", "miRNA sequencing from zebrafish testes and ovaries exposed to normal and high temperatures", "PRJNA755482", "Other", "We exposed zebrafish to elevated temperatures during early development a treatment that is known to result in male skewed sex ratios in order to understand the role of the epigenetic regulation mediated by miRNAs in the gonads.", null, null, null, "Ovary High Temperature", "ZF 36 G6F", null, "strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OHT 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of Danio rerio: adult treated ovary", "36 G6", "36 G6", "NEBNext Small RNA Library Prep Set for Illumina was used on total RNA isolated from zebrafish ovary using Qiagen RNeasy mini kit. Library was constructed using sequencing Lane 1x50 v4 HiSeq single end mode with a read length of 50 bp", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP332839", null, null, "ZF_36_G6_22313_GTCCGC.fastq ZF_36_G6_24794_GTCCGC.fastq", "fastq fastq", 369579500.0, 7391590.0, "ZF 36 G6 22313 GTCCGC.fastq", "0:50 1:0", "A:110926203;C:80638311;G:95343987;T:82657357;N:13642", 50, 0, null, null, 110926203, 80638311, 95343987, 82657357, 13642, "SRX11797835", "SRS9797770", "SRA1279325", "Institute of Marine Sciences|Repro-Immune Team", "Institute of Marine Sciences", 1, 0.74041, null, 0.54329, null, 0.82923, null, 0.52999, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2021-08-17", "Adult", "Adult", "Gonad", "Reproductive System"], [69435, "SRR18685198", "SRX14786396", "SRS12545301", "SRP368241", "PRJNA824784", "Divergent composition and transposon silencing activity of small RNAs in mammalian oocytes", "GSE200470", "Other", "We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species except mouse. We found endo siRNAs resulted from the truncated Dicer isoform were mouse specific and os piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2' three prime O methylation. The sequences of many highly expressed piRNA clusters are fast evolving compared with their syntenic genomic locations and the TE families distributing in the conserved piRNA clusters are various between species. Overall design: Profiling small RNAs and mRNA in oocytes from 12 animals.", null, "pubmed:38532500", null, "small RNA zebrafish 3", "GSM6034594", null, "source name:oocyte|tissue:oocyte|Sex:female|Stage:MII|genotype:wild type|molecule subtype:small RNA|geo loc name:missing|collection date:missing", "small RNA zebrafish 3", "We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs tsRNA tRNA derived small non coding RNA rsRNA rRNA derived small non coding RNA small snoRNAs lncRNA and mRNA successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others. We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM transcripts per kilobase of exon model per million mapped reads by StringTie. Assembly: GRCh38 GRCm38 Supplementary files format and content: tab delimited text files include TPM values or raw counts for each Sample", "oocyte", null, "Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 \u00b0C for 3 min and then cooled on ice. For every single oocyte 1 \u03bcl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.", null, "tissue:oocyte|Sex:female|Stage:MII|genotype:wild type|molecule subtype:small RNA", "GSM6034594", "GSM6034594: small RNA zebrafish 3; Danio rerio; miRNA Seq", "GSM6034594 r1", "GSM6034594", "1", "Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 \u00b0C for 3 min and then cooled on ice. For every single oocyte 1 \u03bcl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.", null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP368241", null, null, "Zebrafish3_combined_R1.fastq.gz", "fastq", 687816450.0, 4585443.0, "GSM6034594 r1", "0:150 1:0", "A:94948683;C:106096224;G:367933691;T:118821697;N:16155", 150, 0, null, null, 94948683, 106096224, 367933691, 118821697, 16155, "SRX14786396", "SRS12545301", "SRA1400916", "Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences", "Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences", 1, 2e-05, null, 0.0, null, 0.99993, null, 0.66666, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-08", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [69436, "SRR18685199", "SRX14786395", "SRS12545300", "SRP368241", "PRJNA824784", "Divergent composition and transposon silencing activity of small RNAs in mammalian oocytes", "GSE200470", "Other", "We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species except mouse. We found endo siRNAs resulted from the truncated Dicer isoform were mouse specific and os piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2' three prime O methylation. The sequences of many highly expressed piRNA clusters are fast evolving compared with their syntenic genomic locations and the TE families distributing in the conserved piRNA clusters are various between species. Overall design: Profiling small RNAs and mRNA in oocytes from 12 animals.", null, "pubmed:38532500", null, "small RNA zebrafish 2", "GSM6034593", null, "source name:oocyte|tissue:oocyte|Sex:female|Stage:MII|genotype:wild type|molecule subtype:small RNA|geo loc name:missing|collection date:missing", "small RNA zebrafish 2", "We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs tsRNA tRNA derived small non coding RNA rsRNA rRNA derived small non coding RNA small snoRNAs lncRNA and mRNA successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others. We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM transcripts per kilobase of exon model per million mapped reads by StringTie. Assembly: GRCh38 GRCm38 Supplementary files format and content: tab delimited text files include TPM values or raw counts for each Sample", "oocyte", null, "Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 \u00b0C for 3 min and then cooled on ice. For every single oocyte 1 \u03bcl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.", null, "tissue:oocyte|Sex:female|Stage:MII|genotype:wild type|molecule subtype:small RNA", "GSM6034593", "GSM6034593: small RNA zebrafish 2; Danio rerio; miRNA Seq", "GSM6034593 r1", "GSM6034593", "1", "Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 \u00b0C for 3 min and then cooled on ice. For every single oocyte 1 \u03bcl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.", null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP368241", null, null, "Zebrafish2_combined_R1.fastq.gz", "fastq", 354830850.0, 2365539.0, "GSM6034593 r1", "0:150 1:0", "A:48935028;C:57418354;G:192263153;T:56206000;N:8315", 150, 0, null, null, 48935028, 57418354, 192263153, 56206000, 8315, "SRX14786395", "SRS12545300", "SRA1400916", "Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences", "Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences", 1, 0.00026, null, 0.0, null, 0.99967, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-08", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [69437, "SRR18685200", "SRX14786394", "SRS12545299", "SRP368241", "PRJNA824784", "Divergent composition and transposon silencing activity of small RNAs in mammalian oocytes", "GSE200470", "Other", "We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species except mouse. We found endo siRNAs resulted from the truncated Dicer isoform were mouse specific and os piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2' three prime O methylation. The sequences of many highly expressed piRNA clusters are fast evolving compared with their syntenic genomic locations and the TE families distributing in the conserved piRNA clusters are various between species. Overall design: Profiling small RNAs and mRNA in oocytes from 12 animals.", null, "pubmed:38532500", null, "small RNA zebrafish 1", "GSM6034592", null, "source name:oocyte|tissue:oocyte|Sex:female|Stage:MII|genotype:wild type|molecule subtype:small RNA|geo loc name:missing|collection date:missing", "small RNA zebrafish 1", "We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs tsRNA tRNA derived small non coding RNA rsRNA rRNA derived small non coding RNA small snoRNAs lncRNA and mRNA successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others. We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM transcripts per kilobase of exon model per million mapped reads by StringTie. Assembly: GRCh38 GRCm38 Supplementary files format and content: tab delimited text files include TPM values or raw counts for each Sample", "oocyte", null, "Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 \u00b0C for 3 min and then cooled on ice. For every single oocyte 1 \u03bcl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.", null, "tissue:oocyte|Sex:female|Stage:MII|genotype:wild type|molecule subtype:small RNA", "GSM6034592", "GSM6034592: small RNA zebrafish 1; Danio rerio; miRNA Seq", "GSM6034592 r1", "GSM6034592", "1", "Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 \u00b0C for 3 min and then cooled on ice. For every single oocyte 1 \u03bcl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.", null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP368241", null, null, "Zebrafish1_combined_R1.fastq.gz", "fastq", 1096131600.0, 7307544.0, "GSM6034592 r1", "0:150 1:0", "A:172547981;C:159060763;G:590708513;T:173788947;N:25396", 150, 0, null, null, 172547981, 159060763, 590708513, 173788947, 25396, "SRX14786394", "SRS12545299", "SRA1400916", "Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences", "Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences", 1, 0.00016, null, 0.0, null, 0.99965, null, 0.96551, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-08", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [76734, "SRR25361306", "SRX21100653", "SRS18369835", "SRP450509", "PRJNA996758", "Transcriptome analysis of Zebrafish testis", "PRJNA996758", "Other", "In summary this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.", null, null, null, null, "Zebrafish 3N 3", null, "strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of triploid zebrafish: mature testis 3", "S06", "S06", "small RNA Sample Pre Kit", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP450509", null, null, "Zebrafish-3N-3.fq", "fastq", 377566667.0, 15350070.0, "Zebrafish 3N 3.fq", "0:24.60", "A:96137966;C:76631652;G:87723617;T:117047567;N:25865", 24, null, null, null, 96137966, 76631652, 87723617, 117047567, 25865, "SRX21100653", "SRS18369835", "SRA1676237", "Hunan Normal University|College of Life Sciences", "Hunan Normal University", 1, 0.73654, null, 0.40118, null, 0.8564, null, 0.55134, null, 20, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-20", "Adult", "Adult", "Gonad", "Reproductive System"], [76735, "SRR25361307", "SRX21100652", "SRS18369834", "SRP450509", "PRJNA996758", "Transcriptome analysis of Zebrafish testis", "PRJNA996758", "Other", "In summary this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.", null, null, null, null, "Zebrafish 3N 2", null, "strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of triploid zebrafish: mature testis 2", "S05", "S05", "small RNA Sample Pre Kit", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP450509", null, null, "Zebrafish-3N-2.fq", "fastq", 380484856.0, 15447197.0, "Zebrafish 3N 2.fq", "0:24.63", "A:97242128;C:77738745;G:86938175;T:118539773;N:26035", 24, null, null, null, 97242128, 77738745, 86938175, 118539773, 26035, "SRX21100652", "SRS18369834", "SRA1676237", "Hunan Normal University|College of Life Sciences", "Hunan Normal University", 1, 0.75732, null, 0.36733, null, 0.86003, null, 0.56474, null, 30, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-20", "Adult", "Adult", "Gonad", "Reproductive System"], [76736, "SRR25361308", "SRX21100651", "SRS18369833", "SRP450509", "PRJNA996758", "Transcriptome analysis of Zebrafish testis", "PRJNA996758", "Other", "In summary this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.", null, null, null, null, "Zebrafish 3N 1", null, "strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of triploid zebrafish: mature testis 1", "S04", "S04", "small RNA Sample Pre Kit", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP450509", null, null, "Zebrafish-3N-1.fq", "fastq", 268097774.0, 10780393.0, "Zebrafish 3N 1.fq", "0:24.87", "A:68574209;C:53994512;G:62001426;T:83509528;N:18099", 24, null, null, null, 68574209, 53994512, 62001426, 83509528, 18099, "SRX21100651", "SRS18369833", "SRA1676237", "Hunan Normal University|College of Life Sciences", "Hunan Normal University", 1, 0.76185, null, 0.39184, null, 0.86038, null, 0.55005, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-20", "Adult", "Adult", "Gonad", "Reproductive System"], [76737, "SRR25361309", "SRX21100650", "SRS18369832", "SRP450509", "PRJNA996758", "Transcriptome analysis of Zebrafish testis", "PRJNA996758", "Other", "In summary this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.", null, null, null, null, "Zebrafish 2N 3", null, "strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of diploid zebrafish: mature testis 3", "S03", "S03", "small RNA Sample Pre Kit", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP450509", null, null, "Zebrafish-2N-3.fq", "fastq", 534146242.0, 21237464.0, "Zebrafish 2N 3.fq", "0:25.15", "A:134813196;C:109988603;G:122363487;T:166967106;N:13850", 25, null, null, null, 134813196, 109988603, 122363487, 166967106, 13850, "SRX21100650", "SRS18369832", "SRA1676237", "Hunan Normal University|College of Life Sciences", "Hunan Normal University", 1, 0.78557, null, 0.41489, null, 0.84682, null, 0.52155, null, 26, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-20", "Adult", "Adult", "Gonad", "Reproductive System"], [76738, "SRR25361310", "SRX21100649", "SRS18369831", "SRP450509", "PRJNA996758", "Transcriptome analysis of Zebrafish testis", "PRJNA996758", "Other", "In summary this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.", null, null, null, null, "Zebrafish 2N 2", null, "strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of diploid zebrafish: mature testis 2", "S02", "S02", "small RNA Sample Pre Kit", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP450509", null, null, "Zebrafish-2N-2.fq", "fastq", 356097642.0, 14145771.0, "Zebrafish 2N 2.fq", "0:25.17", "A:90441485;C:73979402;G:81604410;T:110063163;N:9182", 25, null, null, null, 90441485, 73979402, 81604410, 110063163, 9182, "SRX21100649", "SRS18369831", "SRA1676237", "Hunan Normal University|College of Life Sciences", "Hunan Normal University", 1, 0.75286, null, 0.42266, null, 0.8561, null, 0.55388, null, 25, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-20", "Adult", "Adult", "Gonad", "Reproductive System"], [76739, "SRR25361311", "SRX21100648", "SRS18369830", "SRP450509", "PRJNA996758", "Transcriptome analysis of Zebrafish testis", "PRJNA996758", "Other", "In summary this study obtained whole transcriptome data of mature testis of triploid zebrafish by RNA seq which provided a data platform for the study of reproductive development of triploid fish. Screening and identification of miRNAs related to spermatogenesis in zebrafish.", null, null, null, null, "Zebrafish 2N 1", null, "strain:not collected|age:3 mpf|collection date:not collected|geo loc name:not applicable|sex:male|tissue:testis|replicate:biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of diploid zebrafish: mature testis 1", "S01", "S01", "small RNA Sample Pre Kit", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "PCR", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP450509", null, null, "Zebrafish-2N-1.fq", "fastq", 304073792.0, 11993451.0, "Zebrafish 2N 1.fq", "0:25.35", "A:78785751;C:62508430;G:69338558;T:93420600;N:20453", 25, null, null, null, 78785751, 62508430, 69338558, 93420600, 20453, "SRX21100648", "SRS18369830", "SRA1676237", "Hunan Normal University|College of Life Sciences", "Hunan Normal University", 1, 0.77026, null, 0.38872, null, 0.86032, null, 0.58206, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-07-20", "Adult", "Adult", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 72, "expanded_columns": [], "expandable_columns": [], "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": [], "units": {}, "query": {"sql": "select 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], 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