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23 rows where experiment.library_selection = "size fractionation", experiment.library_strategy = "RNA-Seq" and tissue_curation_coarse = "Reproductive System"

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devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Reproductive System · 23 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • RNA-Seq · 23 ✖

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 23 ✖

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
36273 36273 SRR298566 SRX079844 SRS212650 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   WTTESTIS GSM727523   tissue:adult testis extract|strain:TL WTTESTIS three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. adult testis extract   Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727523 GSM727523: WTTESTIS GSM727523: WTTESTIS GSM727523: WTTESTIS 1   GEO Accession:GSM727523 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> SRP007331   read name barcode proc directive:ignore WTTESTIS.fastq fastq 732997980.0 20361055.0 GSM727523 1 0:36   36                 SRX079844 SRS212650 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.08155   0.07176   0.97851   0.52359   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Adult Adult Gonad Reproductive System
36274 36274 SRR298565 SRX079843 SRS212649 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   WT3WK GSM727522   tissue:3 wpf whole gonads|strain:TL WT3WK three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. 3 wpf whole gonads   Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727522 GSM727522: WT3WK GSM727522: WT3WK GSM727522: WT3WK 1   GEO Accession:GSM727522 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> SRP007331   read name barcode proc directive:ignore WT3WK.fastq fastq 365473116.0 10152031.0 GSM727522 1 0:36   36                 SRX079843 SRS212649 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.09055   0.0603   0.97798   0.44571   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Larval Larval Gonad Reproductive System
36275 36275 SRR298564 SRX079842 SRS212648 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   TDRD1WK3 GSM727521   tissue:3 wpf tdrd1 mutant gonads|strain:TL TDRD1WK3 three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. 3 wpf tdrd1 mutant gonads   Tissue was homogenized in trizol and total RNA was isolated. RNAs ranging from 18 35 nucleotides were size selected from gel. For cDNA synthesis the RNA molecules in the immunoprecipitated fraction were first poly A tailed using polyApolymerase followed by ligation of synthetic RNA adapter to the five prime phosphate. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727521 GSM727521: TDRD1WK3 GSM727521: TDRD1WK3 GSM727521: TDRD1WK3 1   GEO Accession:GSM727521 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> SRP007331   read name barcode proc directive:ignore TDRD1WK3.fastq fastq 369931536.0 10275876.0 GSM727521 1 0:36   36                 SRX079842 SRS212648 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.08303   0.04674   0.97938   0.35673   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Larval Larval Gonad Reproductive System
36514 36514 SRR578923 SRX190981 SRS366702 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJD male GSM1014087   source name:Testes|sex:male|strain:SJD|development stage:Adult|tissue:Testes SJD male Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Testes   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:male|strain:SJD|developmental stage:Adult|tissue:Testes GSM1014087 GSM1014087: SJD male; Danio rerio; RNA Seq GSM1014087 1   1   GEO Accession:GSM1014087 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJD_Male.fastq fastq 869956128.0 24165448.0 GSM1014087 r1 0:36 A:216078167;C:187750746;G:231408128;T:234642875;N:76212 36       216078167 187750746 231408128 234642875 76212 SRX190981 SRS366702 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.27444   0.19385   0.92478   0.49214   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36515 36515 SRR578922 SRX190980 SRS366701 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   Tu Male GSM1014086   source name:Testes|sex:male|strain:Tu|development stage:Adult|tissue:Testes Tu Male Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Testes   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:male|strain:Tu|developmental stage:Adult|tissue:Testes GSM1014086 GSM1014086: Tu Male; Danio rerio; RNA Seq GSM1014086 1   1   GEO Accession:GSM1014086 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         908421696.0 25233936.0 GSM1014086 r1 0:36 A:222765185;C:198165182;G:240641436;T:246807325;N:42568 36       222765185 198165182 240641436 246807325 42568 SRX190980 SRS366701 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.1451   0.10199   0.95128   0.45517   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36516 36516 SRR578921 SRX190979 SRS366700 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF2 Individual 2 GSM1014085   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF2 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014085 GSM1014085: TuxSJDF2 Individual 2; Danio rerio; RNA Seq GSM1014085 1   1   GEO Accession:GSM1014085 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         383509188.0 10653033.0 GSM1014085 r1 0:36 A:105355133;C:85084746;G:89408418;T:103592177;N:68714 36       105355133 85084746 89408418 103592177 68714 SRX190979 SRS366700 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.14582   0.10997   0.96175   0.35151   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36517 36517 SRR578920 SRX190978 SRS366699 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF2 Individual 1 GSM1014084   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF2 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014084 GSM1014084: TuxSJDF2 Individual 1; Danio rerio; RNA Seq GSM1014084 1   1   GEO Accession:GSM1014084 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     TuxSJDF1_Individual_1.fastq fastq 464899752.0 12913882.0 GSM1014084 r1 0:36 A:140830427;C:93401413;G:113254459;T:117332119;N:81334 36       140830427 93401413 113254459 117332119 81334 SRX190978 SRS366699 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.43194   0.32   0.93154   0.3438   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36518 36518 SRR578919 SRX190977 SRS366698 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF2 GSM1014083   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014083 GSM1014083: TuxSJDF2; Danio rerio; RNA Seq GSM1014083 1   1   GEO Accession:GSM1014083 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     TuxSJDF2.fastq fastq 1036162620.0 28782295.0 GSM1014083 r1 0:36 A:268457303;C:215700792;G:273583173;T:278046713;N:374639 36       268457303 215700792 273583173 278046713 374639 SRX190977 SRS366698 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.16399   0.12914   0.9517   0.52232   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36519 36519 SRR578918 SRX190976 SRS366697 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF1 Individual 2 GSM1014082   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF1 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014082 GSM1014082: TuxSJDF1 Individual 2; Danio rerio; RNA Seq GSM1014082 1   1   GEO Accession:GSM1014082 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         344764980.0 9576805.0 GSM1014082 r1 0:36 A:90252809;C:80943703;G:83338280;T:90171695;N:58493 36       90252809 80943703 83338280 90171695 58493 SRX190976 SRS366697 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.18861   0.14536   0.95335   0.54431   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36520 36520 SRR578917 SRX190975 SRS366696 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF1 Individual 1 GSM1014081   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF1 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014081 GSM1014081: TuxSJDF1 Individual 1; Danio rerio; RNA Seq GSM1014081 1   1   GEO Accession:GSM1014081 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     TuxSJDF2_Individual_1.fastq fastq 373504320.0 10375120.0 GSM1014081 r1 0:36 A:96550943;C:89937876;G:87356943;T:99426239;N:232319 36       96550943 89937876 87356943 99426239 232319 SRX190975 SRS366696 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.15362   0.12272   0.95943   0.56453   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36521 36521 SRR578916 SRX190974 SRS366695 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   TuxSJDF1 GSM1014080   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary TuxSJDF1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014080 GSM1014080: TuxSJDF1; Danio rerio; RNA Seq GSM1014080 1   1   GEO Accession:GSM1014080 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     TuxSJDF1.fastq fastq 1031108904.0 28641914.0 GSM1014080 r1 0:36 A:270773113;C:213123466;G:267237418;T:279702377;N:272530 36       270773113 213123466 267237418 279702377 272530 SRX190974 SRS366695 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.15469   0.12537   0.95457   0.48819   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36522 36522 SRR578915 SRX190973 SRS366694 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   Tu P0 Individual 2 GSM1014079   source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary Tu P0 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary GSM1014079 GSM1014079: Tu P0 Individual 2; Danio rerio; RNA Seq GSM1014079 1   1   GEO Accession:GSM1014079 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         464586408.0 12905178.0 GSM1014079 r1 0:36 A:150621423;C:99131637;G:92380585;T:122374816;N:77947 36       150621423 99131637 92380585 122374816 77947 SRX190973 SRS366694 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.0937   0.05289   0.96546   0.60026   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36523 36523 SRR578914 SRX190972 SRS366693 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   Tu P0 Individual 1 GSM1014078   source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary Tu P0 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary GSM1014078 GSM1014078: Tu P0 Individual 1; Danio rerio; RNA Seq GSM1014078 1   1   GEO Accession:GSM1014078 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         427172796.0 11865911.0 GSM1014078 r1 0:36 A:135500495;C:91385480;G:87823245;T:112202150;N:261426 36       135500495 91385480 87823245 112202150 261426 SRX190972 SRS366693 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.1368   0.09652   0.95142   0.49555   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36524 36524 SRR578913 SRX190971 SRS366692 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   Tu P0 GSM1014077   source name:Ovary|sex:female|strain:Tu|development stage:Adult|tissue:Ovary Tu P0 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Tu|developmental stage:Adult|tissue:Ovary GSM1014077 GSM1014077: Tu P0; Danio rerio; RNA Seq GSM1014077 1   1   GEO Accession:GSM1014077 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         967772772.0 26882577.0 GSM1014077 r1 0:36 A:227085973;C:218180545;G:249458631;T:273002038;N:45585 36       227085973 218180545 249458631 273002038 45585 SRX190971 SRS366692 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.14418   0.1135   0.95818   0.51074   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36525 36525 SRR578912 SRX190970 SRS366691 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF2 Individual 2 GSM1014076   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF2 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014076 GSM1014076: SJDxTuF2 Individual 2; Danio rerio; RNA Seq GSM1014076 1   1   GEO Accession:GSM1014076 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         347475024.0 9652084.0 GSM1014076 r1 0:36 A:91189258;C:81789488;G:84551251;T:89882775;N:62252 36       91189258 81789488 84551251 89882775 62252 SRX190970 SRS366691 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.15872   0.12439   0.95848   0.56717   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36526 36526 SRR578911 SRX190969 SRS366690 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF2 Individual 1 GSM1014075   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF2 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014075 GSM1014075: SJDxTuF2 Individual 1; Danio rerio; RNA Seq GSM1014075 1   1   GEO Accession:GSM1014075 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         400137228.0 11114923.0 GSM1014075 r1 0:36 A:107143937;C:91495000;G:94706504;T:106722021;N:69766 36       107143937 91495000 94706504 106722021 69766 SRX190969 SRS366690 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.15753   0.12463   0.95538   0.5649   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36527 36527 SRR578910 SRX190968 SRS366689 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF2 GSM1014074   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014074 GSM1014074: SJDxTuF2; Danio rerio; RNA Seq GSM1014074 1   1   GEO Accession:GSM1014074 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJDxTuF2.fastq fastq 958492116.0 26624781.0 GSM1014074 r1 0:36 A:261275440;C:193944805;G:248348765;T:254793050;N:130056 36       261275440 193944805 248348765 254793050 130056 SRX190968 SRS366689 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.20051   0.16387   0.94653   0.53263   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36528 36528 SRR578909 SRX190967 SRS366688 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF1 Individual 2 GSM1014073   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF1 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014073 GSM1014073: SJDxTuF1 Individual 2; Danio rerio; RNA Seq GSM1014073 1   1   GEO Accession:GSM1014073 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         435761532.0 12104487.0 GSM1014073 r1 0:36 A:120580697;C:105605593;G:91379055;T:117787426;N:408761 36       120580697 105605593 91379055 117787426 408761 SRX190967 SRS366688 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.07215   0.05695   0.97557   0.48838   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36529 36529 SRR578908 SRX190966 SRS366687 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF1 Individual 1 GSM1014072   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF1 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014072 GSM1014072: SJDxTuF1 Individual 1; Danio rerio; RNA Seq GSM1014072 1   1   GEO Accession:GSM1014072 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         378296532.0 10508237.0 GSM1014072 r1 0:36 A:109216358;C:76585213;G:90165899;T:102085771;N:243291 36       109216358 76585213 90165899 102085771 243291 SRX190966 SRS366687 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.13684   0.10794   0.96335   0.49651   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36530 36530 SRR578907 SRX190965 SRS366686 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJDxTuF1 GSM1014071   source name:Ovary|sex:female|strain:Hybrid SJD and Tu|development stage:Adult|tissue:Ovary SJDxTuF1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:Hybrid SJD and Tu|developmental stage:Adult|tissue:Ovary GSM1014071 GSM1014071: SJDxTuF1; Danio rerio; RNA Seq GSM1014071 1   1   GEO Accession:GSM1014071 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982         1047688380.0 29102455.0 GSM1014071 r1 0:36 A:277032474;C:213232299;G:269309034;T:288068877;N:45696 36       277032474 213232299 269309034 288068877 45696 SRX190965 SRS366686 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.1858   0.15153   0.95006   0.51345   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36531 36531 SRR578906 SRX190964 SRS366685 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJD P0 Individual 2 GSM1014070   source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary SJD P0 Individual 2 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary GSM1014070 GSM1014070: SJD P0 Individual 2; Danio rerio; RNA Seq GSM1014070 1   1   GEO Accession:GSM1014070 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJD_P0_Individual_2.fastq fastq 392951772.0 10915327.0 GSM1014070 r1 0:36 A:126709476;C:82393458;G:82997127;T:100597122;N:254589 36       126709476 82393458 82997127 100597122 254589 SRX190964 SRS366685 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.12786   0.10199   0.95724   0.52026   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36532 36532 SRR578905 SRX190963 SRS366684 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJD P0 Individual 1 GSM1014069   source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary SJD P0 Individual 1 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary GSM1014069 GSM1014069: SJD P0 Individual 1; Danio rerio; RNA Seq GSM1014069 1   1   GEO Accession:GSM1014069 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJD_P0_Individual_1.fastq fastq 379882512.0 10552292.0 GSM1014069 r1 0:36 A:122444116;C:80302064;G:76948943;T:99839311;N:348078 36       122444116 80302064 76948943 99839311 348078 SRX190963 SRS366684 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.21364   0.16206   0.94268   0.45306   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 Adult Adult Gonad Reproductive System
36533 36533 SRR578904 SRX190962 SRS366683 SRP015982 PRJNA176481 Small RNA analysis of Tu And SJD zebrafish strain and their progeny GSE41299 Transcriptome Analysis Small RNA libraries from total RNA isolated from adult ovaries Overall design: Small RNA libraries were derived from Ovaries of the Founder strain and their offspring and their reciprocal offspring. RNA from 5 individual ovaries was pooled .   pubmed:23335638   SJD P0 GSM1014068   source name:Ovary|sex:female|strain:SJD|development stage:Adult|tissue:Ovary SJD P0 Barcode splitting and adapter trimming performed using custom scripts. Barcode is the first 4 bases of the reads except for libraries Tu Male Tu P0 SJD Male SJD P0 SJDxTuF1 TuxSJDF1 TuxSJDF2 and SJDxTuF2 which do not have a barcode. three prime adapter seqeunce starts with 'TCGTATG'. Reads were mapped to D.rerio genome assembly using megablast software. Genome build: Zv9 Supplementary files format and content: Text file with read counts Ovary   Total RNA was isolated using fast protK mediated lysis and Trizol LS protocols. five prime and three prime adaptors were ligated. RNA was not treated with any enzymes before ligation steps. Animals were grown under standard conditioni gender:female|strain:SJD|developmental stage:Adult|tissue:Ovary GSM1014068 GSM1014068: SJD P0; Danio rerio; RNA Seq GSM1014068 1   1   GEO Accession:GSM1014068 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer IIx   SRP015982     SJD_P0.fastq fastq 837950832.0 23276412.0 GSM1014068 r1 0:36 A:217386642;C:179519865;G:217337232;T:223633685;N:73408 36       217386642 179519865 217337232 223633685 73408 SRX190962 SRS366683 SRA059229 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.26607   0.21631   0.93789   0.46928   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   Netherlands 2012-10-03 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");;