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72 rows where experiment.library_strategy = "miRNA-Seq" and tissue_curation_coarse = "Reproductive System"

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devstage_curation 6

experiment.library_selection 5

devstage_curation_coarse 3

tissue_curation 2

experiment.platform 2

tissue_curation_coarse 1

  • Reproductive System · 72 ✖

technology 1

experiment.library_strategy 1

  • miRNA-Seq · 72 ✖

experiment.library_source 1

experiment.library_layout 1

Link 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
15550 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 10–300 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.       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                 Ion Torrent Proton sequencing ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1 RID0024 1     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ION_TORRENT Ion Torrent Proton   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 AMSTERDAM 01 10 2014 14:25:29:391 1 0:75.07 A:1523328157;C:1795624453;G:1849675240;T:1516139338;N:0 75       1523328157 1795624453 1849675240 1516139338 0 ERX604031 ERS557915 ERA363845 UNIVERSITY OF AMSTERDAM UNIVERSITY OF AMSTERDAM 1 0.89536   0.15322   0.91421   0.69019   73   B   usable mapping rate ion_torrent ion_torrent unknown small_rna unknown bulk unknown unknown   Netherlands 2014-10-01 Zygote Embryo Oocyte Reproductive System
37921 37921 SRR1554495 SRX685396 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.   pubmed:24835514     ZF4Ovary1   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                 Zebrafish Ovary2 ZF4Ovary2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF4_Ovary_3.fq.gz fastq 1225610154.0 12134754.0 Ovary2 Run3 0:101 A:347141358;C:303255805;G:280185540;T:294456010;N:571441 101       347141358 303255805 280185540 294456010 571441 SRX685396 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 2e-05   1e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37922 37922 SRR1554492 SRX685395 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.   pubmed:24835514     ZF2Testis1   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                 Zebrafish Testis2 ZF2Testis2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     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       373380865 276125943 251033102 290931637 552875 SRX685395 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 3e-05   1e-05   0.99997   0.0   101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37925 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.   pubmed:24835514     ZF3Ovary1   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                 Zebrafish Ovary1 ZF3Ovary2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     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       107805981 80183725 73617313 85763181 145954 SRX685391 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 5e-05   4e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37926 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 AB.   pubmed:24835514     ZF1Testis1   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                 Zebrafish Testis1 ZF1Testis2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF1_Testis_3.fq.gz fastq 1184228636.0 11725036.0 Testis1 Run3 0:101 A:340636900;C:278505979;G:259975802;T:304564724;N:545231 101       340636900 278505979 259975802 304564724 545231 SRX685390 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 1e-05   0.0   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37929 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.   pubmed:24835514     ZF4Ovary1   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                 Zebrafish Ovary2 ZF4Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     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       111060704 120863975 129849761 114224677 105161 SRX683354 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00027   8e-05   0.99945   0.8125   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37930 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.   pubmed:24835514     ZF4Ovary1   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                 Zebrafish Ovary2 ZF4Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     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       129925815 148479658 148478706 132824290 2247883 SRX683354 SRS686645 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00022   0.0001   0.99967   0.6875   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37931 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.   pubmed:24835514     ZF2Testis1   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                 Zebrafish Testis2 ZF2Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     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       145360493 148943988 151402108 140286245 159397 SRX683353 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 8e-05   2e-05   0.99985   0.57142   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37932 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.   pubmed:24835514     ZF2Testis1   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                 Zebrafish Testis2 ZF2Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     ZF2_Testis_2.fq.gz fastq 697016337.0 13666987.0 Testis2 Run2 0:51 A:172082858;C:184634425;G:173370430;T:163527914;N:3400710 51       172082858 184634425 173370430 163527914 3400710 SRX683353 SRS686644 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 8e-05   2e-05   0.99985   0.57142   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37937 37937 SRR1554481 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.   pubmed:24835514     ZF3Ovary1   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                 Zebrafish Ovary1 ZF3Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     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       29237121 30235277 29264328 27320814 29425 SRX683080 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00022   9e-05   0.99967   0.65   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37938 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.   pubmed:24835514     ZF3Ovary1   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                 Zebrafish Ovary1 ZF3Ovary1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     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       34695180 38015933 33434207 32057083 703441 SRX683080 SRS686559 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00016   5e-05   0.99977   0.42857   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37939 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.   pubmed:24835514     ZF1Testis1   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                 Zebrafish Testis1 ZF1Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     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       152422885 163771947 179144090 159997538 179290 SRX683062 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0011   0.00053   0.99829   0.67777   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37940 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.   pubmed:24835514     ZF1Testis1   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                 Zebrafish Testis1 ZF1Testis1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP039502     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       180116528 202508153 204833105 186435696 3700917 SRX683062 SRS686542 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.00073   0.00032   0.99898   0.62745   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Gonad Reproductive System
37997 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.   pubmed:26574018   Testis Replicate 3 sRNAseq GSM1376643   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 Friedländer 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 <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> 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™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   SRP041544     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       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   0.00333   0.99845   0.7331   76   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gonad Reproductive System
37998 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.   pubmed:26574018   Testis Replicate 2 sRNAseq GSM1376642   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 Friedländer 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 <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> 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™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   SRP041544     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       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   0.00651   0.99788   0.69591   76   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gonad Reproductive System
37999 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.   pubmed:26574018   Testis Replicate 1 sRNAseq GSM1376641   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 Friedländer 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 <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> 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™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   SRP041544     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       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   3e-05   0.99943   0.69387   76   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gonad Reproductive System
38000 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.   pubmed:26574018   Ovary Replicate 3 sRNAseq GSM1376640   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 Friedländer 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 <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> 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™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   SRP041544     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       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   0.00068   0.99513   0.75483   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gonad Reproductive System
38001 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.   pubmed:26574018   Ovary Replicate 2 sRNAseq GSM1376639   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 Friedländer 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 <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> 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™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   SRP041544     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       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   0.00355   0.98212   0.67744   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gonad Reproductive System
38002 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.   pubmed:26574018   Ovary Replicate 1 sRNAseq GSM1376638   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 Friedländer 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 <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> 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™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   1 Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ 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 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ 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   SRP041544     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       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   0.0004   0.99644   0.84584   51   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Singapore 2014-04-29 Undetermined Embryo Gonad Reproductive System
38256 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   pubmed:26418264   zebrafish sperm GSM1517943   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’ adaptor 5’ 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   Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer’s 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.   cell type:Spermatozoa|strain:AB wild type GSM1517943 GSM1517943: zebrafish sperm; Danio rerio; miRNA Seq GSM1517943   1 Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer’s 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   SRP048591     zebrafish-sperm5.fq.bz2 fastq 588000000.0 12000000.0 GSM1517943 r1 0:49 A:122673394;C:136175879;G:140377184;T:188702650;N:70893 49       122673394 136175879 140377184 188702650 70893 SRX719267 SRS715451 SRA188511 GEO SUN YAT-SEN UNIVERSITY 1 2e-05   0.0   0.99997   1.0   49   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2014-10-02 Zygote Embryo Oocyte Reproductive System
52326 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 expr…   pubmed:31417497   IIIb 3 GSM3816534   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIb GSM3816534 GSM3816534: IIIb 3; Danio rerio; miRNA Seq GSM3816534   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   SRP199448     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     351029701 324452324 401722902 371889768 246205 SRX5893495 SRS4815090 SRA890399 GEO Biology, YorkU 1 0.08662   0.01333   0.96213   0.83838   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52327 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 expr…   pubmed:31417497   IIIb 3 GSM3816534   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIb GSM3816534 GSM3816534: IIIb 3; Danio rerio; miRNA Seq GSM3816534   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   SRP199448     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     350650304 324162528 401055729 371582418 170121 SRX5893495 SRS4815090 SRA890399 GEO Biology, YorkU 1 0.08676   0.01312   0.96282   0.84604   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52328 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 expr…   pubmed:31417497   IIIb 2 GSM3816533   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIb GSM3816533 GSM3816533: IIIb 2; Danio rerio; miRNA Seq GSM3816533   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   SRP199448     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     242873339 228078637 287889366 253526026 171382 SRX5893494 SRS4815089 SRA890399 GEO Biology, YorkU 1 0.04745   0.00802   0.968   0.75298   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52329 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 expr…   pubmed:31417497   IIIb 2 GSM3816533   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIb GSM3816533 GSM3816533: IIIb 2; Danio rerio; miRNA Seq GSM3816533   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   SRP199448     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     242471282 227664296 287157957 253147388 118477 SRX5893494 SRS4815089 SRA890399 GEO Biology, YorkU 1 0.04679   0.008   0.96946   0.71268   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52330 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 expr…   pubmed:31417497   IIIb 1 GSM3816532   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIb GSM3816532 GSM3816532: IIIb 1; Danio rerio; miRNA Seq GSM3816532   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   SRP199448     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     350805103 319766230 407583206 365448522 243889 SRX5893493 SRS4815088 SRA890399 GEO Biology, YorkU 1 0.02559   0.00389   0.98407   0.82023   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52331 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 expr…   pubmed:31417497   IIIb 1 GSM3816532   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIb GSM3816532 GSM3816532: IIIb 1; Danio rerio; miRNA Seq GSM3816532   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   SRP199448     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     350607715 319569609 407049947 365297986 168993 SRX5893493 SRS4815088 SRA890399 GEO Biology, YorkU 1 0.02565   0.00409   0.98417   0.81633   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52332 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 expr…   pubmed:31417497   IIIa 3 GSM3816531   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIa GSM3816531 GSM3816531: IIIa 3; Danio rerio; miRNA Seq GSM3816531   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   SRP199448     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     333465386 289207984 364882545 336711699 221486 SRX5893492 SRS4815087 SRA890399 GEO Biology, YorkU 1 0.02703   0.00432   0.98313   0.75385   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52333 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 expr…   pubmed:31417497   IIIa 3 GSM3816531   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIa GSM3816531 GSM3816531: IIIa 3; Danio rerio; miRNA Seq GSM3816531   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   SRP199448     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     333031673 288843797 364209143 336315522 154515 SRX5893492 SRS4815087 SRA890399 GEO Biology, YorkU 1 0.02671   0.00422   0.98283   0.76748   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52334 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 expr…   pubmed:31417497   IIIa 2 GSM3816530   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIa GSM3816530 GSM3816530: IIIa 2; Danio rerio; miRNA Seq GSM3816530   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   SRP199448     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     342206537 301597185 385756857 352517232 230789 SRX5893491 SRS4815086 SRA890399 GEO Biology, YorkU 1 0.05315   0.00892   0.9643   0.79967   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52335 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 expr…   pubmed:31417497   IIIa 2 GSM3816530   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIa GSM3816530 GSM3816530: IIIa 2; Danio rerio; miRNA Seq GSM3816530   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   SRP199448     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     342441286 301828080 385820344 352800933 160107 SRX5893491 SRS4815086 SRA890399 GEO Biology, YorkU 1 0.0533   0.00892   0.96323   0.81292   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52336 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 expr…   pubmed:31417497   IIIa 1 GSM3816529   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIa GSM3816529 GSM3816529: IIIa 1; Danio rerio; miRNA Seq GSM3816529   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   SRP199448     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     320039883 296663387 380656068 336233800 225312 SRX5893490 SRS4815085 SRA890399 GEO Biology, YorkU 1 0.0976   0.019   0.93718   0.75404   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
52337 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 expr…   pubmed:31417497   IIIa 1 GSM3816529   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   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   tissue:ovary|cell type:follicular cells|developmental stage:IIIa GSM3816529 GSM3816529: IIIa 1; Danio rerio; miRNA Seq GSM3816529   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   SRP199448     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     320194547 296827909 380547854 336424243 158197 SRX5893490 SRS4815085 SRA890399 GEO Biology, YorkU 1 0.09727   0.01947   0.93866   0.76527   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Canada 2019-05-24 Undetermined Undetermined Gonad Reproductive System
60887 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   pubmed:33506864   h24 2: PGCs 24hpf repeat2 GSM4777194   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 … PGCs   PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.   cell type:primordial germ cells|strain:AB|tissue:gonad GSM4777194 GSM4777194: h24 2: PGCs 24hpf repeat2; Danio rerio; miRNA Seq GSM4777194   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   SRP282187     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     1030703487 1025857271 1004392553 963376583 68856 SRX9110497 SRS7353480 SRA1124474 GEO Shanghai Institute of Biochemistry and Cell Biology,CAS 1 0.00025   0.0   0.99997   1.0   150   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2020-09-12 Pharyngula Embryo Gonad Reproductive System
60888 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   pubmed:33506864   h24 1: PGCs 24hpf repeat1 GSM4777193   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 … PGCs   PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.   cell type:primordial germ cells|strain:AB|tissue:gonad GSM4777193 GSM4777193: h24 1: PGCs 24hpf repeat1; Danio rerio; miRNA Seq GSM4777193   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   SRP282187     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     510125618 561938103 577742482 573267493 37754 SRX9110496 SRS7353479 SRA1124474 GEO Shanghai Institute of Biochemistry and Cell Biology,CAS 1 0.0004   0.0   0.99993   1.0   150   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2020-09-12 Pharyngula Embryo Gonad Reproductive System
60889 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   pubmed:33506864   h11 2: PGCs 11hpf repeat2 GSM4777192   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 … PGCs   PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.   cell type:primordial germ cells|strain:AB|tissue:gonad GSM4777192 GSM4777192: h11 2: PGCs 11hpf repeat2; Danio rerio; miRNA Seq GSM4777192   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   SRP282187     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     419294958 415643261 432730446 457808038 29397 SRX9110495 SRS7353478 SRA1124474 GEO Shanghai Institute of Biochemistry and Cell Biology,CAS 1 0.00062   0.0   0.99991   1.0   150   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2020-09-12 Segmentation Embryo Gonad Reproductive System
60890 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   pubmed:33506864   h11 1: PGCs 11hpf repeat1 GSM4777191   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 … PGCs   PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.   cell type:primordial germ cells|strain:AB|tissue:gonad GSM4777191 GSM4777191: h11 1: PGCs 11hpf repeat1; Danio rerio; miRNA Seq GSM4777191   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   SRP282187     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     722881530 687611993 633563837 646263376 45814 SRX9110494 SRS7353477 SRA1124474 GEO Shanghai Institute of Biochemistry and Cell Biology,CAS 1 0.0006   0.0   0.99991   1.0   150   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2020-09-12 Segmentation Embryo Gonad Reproductive System
60891 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   pubmed:33506864   h6 2: PGCs 6hpf repeat2 GSM4777190   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 … PGCs   PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.   cell type:primordial germ cells|strain:AB|tissue:gonad GSM4777190 GSM4777190: h6 2: PGCs 6hpf repeat2; Danio rerio; miRNA Seq GSM4777190   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   SRP282187     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     563758043 619336180 552040747 595747277 39903 SRX9110493 SRS7353476 SRA1124474 GEO Shanghai Institute of Biochemistry and Cell Biology,CAS 1 0.00014   0.0   0.99997   1.0   150   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2020-09-12 Gastrula Embryo Gonad Reproductive System
60892 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   pubmed:33506864   h6 1: PGCs 6hpf repeat1 GSM4777189   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 … PGCs   PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.   cell type:primordial germ cells|strain:AB|tissue:gonad GSM4777189 GSM4777189: h6 1: PGCs 6hpf repeat1; Danio rerio; miRNA Seq GSM4777189   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   SRP282187     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     453046525 471873747 495904656 558729697 33775 SRX9110492 SRS7353475 SRA1124474 GEO Shanghai Institute of Biochemistry and Cell Biology,CAS 1 0.00028   0.0   0.99997   1.0   150   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   China 2020-09-12 Gastrula Embryo Gonad Reproductive System
64249 64249 SRR14373546 SRX10725858 SRS8815710 SRP318063 PRJNA726592 GH overexpression on gonadal microRNAome profile in zebrafish males PRJNA726592 Other Evaluate computationally the kinetic parameters as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.       gh transgenic 6 GH3   strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:6|BioSampleModel:Model organism or animal                 miRNA Seq of Danio rerio: adult male gonad GH3 GH3 NEBNext Small RNA Library Prep Set     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina MiSeq   SRP318063     PoolUFPEL-GH6.fastq fastq 20104659.0 394209.0 PoolUFPEL GH6.fastq 0:51 1:0 A:4462767;C:4536250;G:6471518;T:4633666;N:458 51 0     4462767 4536250 6471518 4633666 458 SRX10725858 SRS8815710 SRA1226279 Universidade Federal de Pelotas|CDTec Universidade Federal de Pelotas 1 0.80185   0.21091   0.91547   0.57044   51   B   usable mapping rate illumina miseq unknown random_priming nebnext bulk unknown unknown   Brazil 2021-04-30 Adult Adult Gonad Reproductive System
64250 64250 SRR14373547 SRX10725857 SRS8815709 SRP318063 PRJNA726592 GH overexpression on gonadal microRNAome profile in zebrafish males PRJNA726592 Other Evaluate computationally the kinetic parameters as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.       gh transgenic 4 GH2   strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:5|BioSampleModel:Model organism or animal                 miRNA Seq of Danio rerio: adult male gonad GH2 GH2 NEBNext Small RNA Library Prep Set     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina MiSeq   SRP318063     PoolUFPEL-GH4.fastq fastq 136130934.0 2669234.0 PoolUFPEL GH4.fastq 0:51 1:0 A:31505752;C:32606264;G:41632000;T:30383900;N:3018 51 0     31505752 32606264 41632000 30383900 3018 SRX10725857 SRS8815709 SRA1226279 Universidade Federal de Pelotas|CDTec Universidade Federal de Pelotas 1 0.78619   0.26843   0.87834   0.48728   51   B   usable mapping rate illumina miseq unknown random_priming nebnext bulk unknown unknown   Brazil 2021-04-30 Adult Adult Gonad Reproductive System
64251 64251 SRR14373548 SRX10725856 SRS8815708 SRP318063 PRJNA726592 GH overexpression on gonadal microRNAome profile in zebrafish males PRJNA726592 Other Evaluate computationally the kinetic parameters as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.       gh transgenic 3 GH1   strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:4|BioSampleModel:Model organism or animal                 miRNA Seq of Danio rerio: adult male gonad GH1 GH1 NEBNext Small RNA Library Prep Set     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina MiSeq   SRP318063     PoolUFPEL-GH3.fastq fastq 364152699.0 7140249.0 PoolUFPEL GH3.fastq 0:51 1:0 A:79211373;C:83789471;G:117772711;T:83370974;N:8170 51 0     79211373 83789471 117772711 83370974 8170 SRX10725856 SRS8815708 SRA1226279 Universidade Federal de Pelotas|CDTec Universidade Federal de Pelotas 1 0.80843   0.18707   0.92066   0.59133   51   B   usable mapping rate illumina miseq unknown random_priming nebnext bulk unknown unknown   Brazil 2021-04-30 Adult Adult Gonad Reproductive System
64252 64252 SRR14373549 SRX10725855 SRS8815707 SRP318063 PRJNA726592 GH overexpression on gonadal microRNAome profile in zebrafish males PRJNA726592 Other Evaluate computationally the kinetic parameters as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.       Non transgenic 5 NT3   strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:3|BioSampleModel:Model organism or animal                 miRNA Seq of Danio rerio: adult male gonad NT3 NT3 NEBNext Small RNA Library Prep Set     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina MiSeq   SRP318063     PoolUFPEL-NT5.fastq fastq 234366114.0 4595414.0 PoolUFPEL NT5.fastq 0:51 1:0 A:58011123;C:51898677;G:69581397;T:54869614;N:5303 51 0     58011123 51898677 69581397 54869614 5303 SRX10725855 SRS8815707 SRA1226279 Universidade Federal de Pelotas|CDTec Universidade Federal de Pelotas 1 0.83352   0.35958   0.85928   0.50004   51   B   usable mapping rate illumina miseq unknown random_priming nebnext bulk unknown unknown   Brazil 2021-04-30 Adult Adult Gonad Reproductive System
64253 64253 SRR14373550 SRX10725854 SRS8815706 SRP318063 PRJNA726592 GH overexpression on gonadal microRNAome profile in zebrafish males PRJNA726592 Other Evaluate computationally the kinetic parameters as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.       Non transgenic 3 NT2   strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:2|BioSampleModel:Model organism or animal                 miRNA Seq of Danio rerio: adult male gonad NT2 NT2 NEBNext Small RNA Library Prep Set     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina MiSeq   SRP318063     PoolUFPEL-NT3.fastq fastq 147963750.0 2901250.0 PoolUFPEL NT3.fastq 0:51 1:0 A:37528568;C:33498521;G:41979920;T:34953411;N:3330 51 0     37528568 33498521 41979920 34953411 3330 SRX10725854 SRS8815706 SRA1226279 Universidade Federal de Pelotas|CDTec Universidade Federal de Pelotas 1 0.75277   0.34872   0.86596   0.53154   51   B   usable mapping rate illumina miseq unknown random_priming nebnext bulk unknown unknown   Brazil 2021-04-30 Adult Adult Gonad Reproductive System
64254 64254 SRR14373551 SRX10725853 SRS8815705 SRP318063 PRJNA726592 GH overexpression on gonadal microRNAome profile in zebrafish males PRJNA726592 Other Evaluate computationally the kinetic parameters as well as to identify and quantify the set of miRNAs of the spermatozoa from gh transgenic gh+ and non transgenic NT zebrafish that may be correlated with low spermatic quality.       Non transgenic 1 NT1   strain:F0104|age:15 month|dev stage:adult|sex:male|tissue:gonadal|biological replicate:1|BioSampleModel:Model organism or animal                 miRNA Seq of Danio rerio: adult male gonad NT1 NT1 NEBNext Small RNA Library Prep Set     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA Illumina MiSeq   SRP318063     PoolUFPEL-NT1.fastq fastq 218363538.0 4281638.0 PoolUFPEL NT1.fastq 0:51 1:0 A:53115431;C:47639482;G:65248144;T:52355651;N:4830 51 0     53115431 47639482 65248144 52355651 4830 SRX10725853 SRS8815705 SRA1226279 Universidade Federal de Pelotas|CDTec Universidade Federal de Pelotas 1 0.83996   0.3606   0.87728   0.50828   51   B   usable mapping rate illumina miseq unknown random_priming nebnext bulk unknown unknown   Brazil 2021-04-30 Adult Adult Gonad Reproductive System
65669 65669 SRR15498138 SRX11797853 SRS9797787 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.       Ovary High Temperature ZF 36 G12F   strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OHT 2|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult treated ovary 36 G12 36 G12 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_36_G12_22313_ATGAGC.fastq ZF_36_G12_24794_ATGAGC.fastq fastq fastq 385298900.0 7705978.0 ZF 36 G12 22313 ATGAGC.fastq 0:50 1:0 A:115879319;C:84755497;G:100335882;T:84312716;N:15486 50 0     115879319 84755497 100335882 84312716 15486 SRX11797853 SRS9797787 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.76472   0.49644   0.83287   0.51149   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65670 65670 SRR15498139 SRX11797852 SRS9797788 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.       Ovary High Temperature ZF 36 G9F   strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OHT 1|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult treated ovary 36 G9 36 G9 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_36_G9_22313_ACTGAT.fastq ZF_36_G9_24794_ACTGAT.fastq fastq fastq 448040450.0 8960809.0 ZF 36 G9 22313 ACTGAT.fastq 0:50 1:0 A:134152732;C:98754272;G:116124383;T:98987716;N:21347 50 0     134152732 98754272 116124383 98987716 21347 SRX11797852 SRS9797788 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.73407   0.52835   0.83092   0.53201   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65671 65671 SRR15498140 SRX11797851 SRS9797786 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.       Testis Low Temperature ZF 28 G11M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate TLT 2|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated testis 28 G11 28 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G11_22312_CACCGG.fastq fastq 397315650.0 7946313.0 ZF 28 G11 22312 CACCGG.fastq 0:50 1:0 A:117553892;C:87676340;G:103796431;T:88242064;N:46923 50 0     117553892 87676340 103796431 88242064 46923 SRX11797851 SRS9797786 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.7153   0.45777   0.85131   0.51595   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65672 65672 SRR15498141 SRX11797850 SRS9797785 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.       Testis Low Temperature ZF 28 G18M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate TLT 1|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated testis 28 G18 28 G18 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G18_22312_CAACTA.fastq fastq 299844950.0 5996899.0 ZF 28 G18 22312 CAACTA.fastq 0:50 1:0 A:88371816;C:66221559;G:79693659;T:65522293;N:35623 50 0     88371816 66221559 79693659 65522293 35623 SRX11797850 SRS9797785 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.70252   0.44336   0.85782   0.53663   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65673 65673 SRR15498142 SRX11797849 SRS9797784 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.       Ovary Low Temperature ZF 28 G19F   strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OLT 4|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated ovary 28 G19 28 G19 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G19_22312_GTTTCG.fastq ZF_28_G19_24794_GTTTCG.fastq fastq fastq 453746250.0 9074925.0 ZF 28 G19 22312 GTTTCG.fastq 0:50 1:0 A:133375616;C:101583110;G:121165582;T:97585655;N:36287 50 0     133375616 101583110 121165582 97585655 36287 SRX11797849 SRS9797784 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.72934   0.45973   0.81659   0.55084   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65674 65674 SRR15498143 SRX11797848 SRS9797782 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.       Ovary Low Temperature ZF 28 G17F   strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OLT 3|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated ovary 28 G17 28 G17 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G17_22312_GTGGCC.fastq ZF_28_G17_24794_GTGGCC.fastq fastq fastq 400680350.0 8013607.0 ZF 28 G17 22312 GTGGCC.fastq 0:50 1:0 A:116055791;C:92144972;G:109622335;T:82823767;N:33485 50 0     116055791 92144972 109622335 82823767 33485 SRX11797848 SRS9797782 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.67985   0.39457   0.82678   0.60177   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65675 65675 SRR15498144 SRX11797847 SRS9797783 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.       Ovary Low Temperature ZF 28 G8F   strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OLT 2|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated ovary 28 G8 28 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G8_22312_GTAGAG.fastq ZF_28_G8_24794_GTAGAG.fastq fastq fastq 436150900.0 8723018.0 ZF 28 G8 22312 GTAGAG.fastq 0:50 1:0 A:129619390;C:96543331;G:116417612;T:93533768;N:36799 50 0     129619390 96543331 116417612 93533768 36799 SRX11797847 SRS9797783 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.74469   0.47759   0.82637   0.51178   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65676 65676 SRR15498145 SRX11797846 SRS9797780 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.       Ovary Low Temperature ZF 28 G5F   strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OLT 1|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated ovary 28 G5 28 G5 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G5_22312_CCGTCC.fastq ZF_28_G5_24794_CCGTCC.fastq fastq fastq 452563650.0 9051273.0 ZF 28 G5 22312 CCGTCC.fastq 0:50 1:0 A:134503401;C:100875999;G:120893992;T:96252318;N:37940 50 0     134503401 100875999 120893992 96252318 37940 SRX11797846 SRS9797780 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.78672   0.47976   0.82207   0.50024   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65677 65677 SRR15498146 SRX11797845 SRS9797781 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.       Testis Low Temperature ZF 28 G9M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate TLT 4|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated testis 28 G9 28 G9 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G9_22312_CGTACG.fastq ZF_28_G9_24794_CGTACG.fastq fastq fastq 449330450.0 8986609.0 ZF 28 G9 22312 CGTACG.fastq 0:50 1:0 A:134080706;C:98827246;G:115871708;T:100512830;N:37960 50 0     134080706 98827246 115871708 100512830 37960 SRX11797845 SRS9797781 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.7104   0.46962   0.85752   0.51154   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65678 65678 SRR15498147 SRX11797844 SRS9797779 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.       Testis Low Temperature ZF 28 G10M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate TLT 3|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated testis 28 G10 28 G10 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G10_22312_GGTAGC.fastq fastq 326954650.0 6539093.0 ZF 28 G10 22312 GGTAGC.fastq 0:50 1:0 A:96514676;C:71851965;G:86535966;T:72013004;N:39039 50 0     96514676 71851965 86535966 72013004 39039 SRX11797844 SRS9797779 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.69651   0.42268   0.84829   0.52434   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65679 65679 SRR15498148 SRX11797843 SRS9797777 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.       Testis Low Temperature ZF 28 G20M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate TLT 6|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated testis 28 G20 28 G20 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G20_22969_TCGAAG.fastq fastq 589981600.0 11799632.0 ZF 28 G20 22969 TCGAAG.fastq 0:50 1:0 A:174095296;C:129803577;G:155350315;T:130716263;N:16149 50 0     174095296 129803577 155350315 130716263 16149 SRX11797843 SRS9797777 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.73394   0.46125   0.85482   0.51049   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65680 65680 SRR15498149 SRX11797842 SRS9797778 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.       Testis Low Temperature ZF 28 G2M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate TLT 5|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult untreated testis 28 G2 28 G2 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_28_G2_22969_CATTTT.fastq fastq 725495800.0 14509916.0 ZF 28 G2 22969 CATTTT.fastq 0:50 1:0 A:215282734;C:159179418;G:191027998;T:159985829;N:19821 50 0     215282734 159179418 191027998 159985829 19821 SRX11797842 SRS9797778 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.74341   0.46282   0.86365   0.52722   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65681 65681 SRR15498150 SRX11797841 SRS9797776 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.       Testis High Temperature ZF 36 G10M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate THT 4|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult treated testis 36 G10 36 G10 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     ZF_36_G10_22313_ATTCCT.fastq fastq 301310100.0 6026202.0 ZF 36 G10 22313 ATTCCT.fastq 0:50 1:0 A:89802405;C:66792192;G:77376709;T:67302456;N:36338 50 0     89802405 66792192 77376709 67302456 36338 SRX11797841 SRS9797776 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.69865   0.45741   0.86354   0.51584   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65682 65682 SRR15498151 SRX11797840 SRS9797775 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.       Testis High Temperature ZF 36 G15M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate THT 3|BioSampleModel:Model organism or animal                 miRNA seq of Danio rerio: adult treated testis 36 G15 36 G15 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     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     431488151 331693370 386155519 315491607 175053 SRX11797840 SRS9797775 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.72513   0.40489   0.86229   0.50704   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65683 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.       Testis High Temperature ZF 36 G14M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate THT 2|BioSampleModel:Model organism or animal                 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     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     133880771 103643537 119108795 97573024 23623 SRX11797839 SRS9797774 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.67716   0.38799   0.81949   0.53484   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65684 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.       Testis High Temperature ZF 36 G11M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate THT 1|BioSampleModel:Model organism or animal                 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     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     92340462 68123395 79403422 69172711 37010 SRX11797838 SRS9797773 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.68141   0.45311   0.86519   0.52771   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65685 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.       Testis High Temperature ZF 36 G13M   strain:AB|age:90 dpf|sex:male|tissue:Testis|replicate:Biological replicate THT 5|BioSampleModel:Model organism or animal                 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     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     154723201 115780155 137702409 117453866 14169 SRX11797837 SRS9797772 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.74813   0.46889   0.85299   0.51699   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65686 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.       Ovary High Temperature ZF 36 G8F   strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OHT 4|BioSampleModel:Model organism or animal                 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     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     106167879 78499963 93422866 76761338 11154 SRX11797836 SRS9797771 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.74342   0.50048   0.82919   0.51092   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
65687 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.       Ovary High Temperature ZF 36 G6F   strain:AB|age:90 dpf|sex:female|tissue:Ovary|replicate:Biological replicate OHT 3|BioSampleModel:Model organism or animal                 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     miRNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina HiSeq 2500   SRP332839     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     110926203 80638311 95343987 82657357 13642 SRX11797835 SRS9797770 SRA1279325 Institute of Marine Sciences|Repro-Immune Team Institute of Marine Sciences 1 0.74041   0.54329   0.82923   0.52999   50   B   usable mapping rate illumina hiseq_era unknown small_rna nebnext bulk unknown unknown   United States 2021-08-17 Adult Adult Gonad Reproductive System
69435 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.   pubmed:38532500   small RNA zebrafish 3 GSM6034594   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   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 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ 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 °C for 3 min and then cooled on ice. For every single oocyte 1 μl 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.   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 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ 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 °C for 3 min and then cooled on ice. For every single oocyte 1 μl 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.   miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP368241     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     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   0.0   0.99993   0.66666   150   T   under 1.2% mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   China 2022-04-08 Zygote Embryo Oocyte Reproductive System
69436 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.   pubmed:38532500   small RNA zebrafish 2 GSM6034593   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   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 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ 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 °C for 3 min and then cooled on ice. For every single oocyte 1 μl 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.   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 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ 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 °C for 3 min and then cooled on ice. For every single oocyte 1 μl 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.   miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP368241     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     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   0.0   0.99967   1.0   150   T   under 1.2% mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   China 2022-04-08 Zygote Embryo Oocyte Reproductive System
69437 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.   pubmed:38532500   small RNA zebrafish 1 GSM6034592   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   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 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ 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 °C for 3 min and then cooled on ice. For every single oocyte 1 μl 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.   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 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ 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 °C for 3 min and then cooled on ice. For every single oocyte 1 μl 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.   miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina NovaSeq 6000   SRP368241     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     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   0.0   0.99965   0.96551   150   T   under 1.2% mapping rate illumina novaseq_era unknown size_fractionation unknown bulk unknown unknown   China 2022-04-08 Zygote Embryo Oocyte Reproductive System
76734 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.         Zebrafish 3N 3   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                 miRNA Seq of triploid zebrafish: mature testis 3 S06 S06 small RNA Sample Pre Kit     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA HiSeq X Ten   SRP450509     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       96137966 76631652 87723617 117047567 25865 SRX21100653 SRS18369835 SRA1676237 Hunan Normal University|College of Life Sciences Hunan Normal University 1 0.73654   0.40118   0.8564   0.55134   20   B   usable mapping rate illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2023-07-20 Adult Adult Gonad Reproductive System
76735 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.         Zebrafish 3N 2   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                 miRNA Seq of triploid zebrafish: mature testis 2 S05 S05 small RNA Sample Pre Kit     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA HiSeq X Ten   SRP450509     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       97242128 77738745 86938175 118539773 26035 SRX21100652 SRS18369834 SRA1676237 Hunan Normal University|College of Life Sciences Hunan Normal University 1 0.75732   0.36733   0.86003   0.56474   30   B   usable mapping rate illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2023-07-20 Adult Adult Gonad Reproductive System
76736 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.         Zebrafish 3N 1   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                 miRNA Seq of triploid zebrafish: mature testis 1 S04 S04 small RNA Sample Pre Kit     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA HiSeq X Ten   SRP450509     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       68574209 53994512 62001426 83509528 18099 SRX21100651 SRS18369833 SRA1676237 Hunan Normal University|College of Life Sciences Hunan Normal University 1 0.76185   0.39184   0.86038   0.55005   27   B   usable mapping rate illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2023-07-20 Adult Adult Gonad Reproductive System
76737 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.         Zebrafish 2N 3   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                 miRNA Seq of diploid zebrafish: mature testis 3 S03 S03 small RNA Sample Pre Kit     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA HiSeq X Ten   SRP450509     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       134813196 109988603 122363487 166967106 13850 SRX21100650 SRS18369832 SRA1676237 Hunan Normal University|College of Life Sciences Hunan Normal University 1 0.78557   0.41489   0.84682   0.52155   26   B   usable mapping rate illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2023-07-20 Adult Adult Gonad Reproductive System
76738 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.         Zebrafish 2N 2   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                 miRNA Seq of diploid zebrafish: mature testis 2 S02 S02 small RNA Sample Pre Kit     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA HiSeq X Ten   SRP450509     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       90441485 73979402 81604410 110063163 9182 SRX21100649 SRS18369831 SRA1676237 Hunan Normal University|College of Life Sciences Hunan Normal University 1 0.75286   0.42266   0.8561   0.55388   25   B   usable mapping rate illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2023-07-20 Adult Adult Gonad Reproductive System
76739 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.         Zebrafish 2N 1   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                 miRNA Seq of diploid zebrafish: mature testis 1 S01 S01 small RNA Sample Pre Kit     miRNA-Seq TRANSCRIPTOMIC PCR SINGLE ILLUMINA HiSeq X Ten   SRP450509     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       78785751 62508430 69338558 93420600 20453 SRX21100648 SRS18369830 SRA1676237 Hunan Normal University|College of Life Sciences Hunan Normal University 1 0.77026   0.38872   0.86032   0.58206   23   B   usable mapping rate illumina hiseq_era full_length random_priming unknown bulk unknown unknown   China 2023-07-20 Adult Adult Gonad Reproductive System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;