{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", experiment.library_strategy = \"ncRNA-Seq\" and tissue_curation = \"Gonad\"", "rows": [[41150, "SRR3744678", "SRX1898686", "SRS1541536", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto homozygous 5", "GSM2226636", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / ", "moto homozygous 5", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / ", "GSM2226636", "GSM2226636: moto homozygous 5; Danio rerio; ncRNA Seq", "GSM2226636", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226636", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 2118467988.0, 41538588.0, "GSM2226636 r1", "0:51", "A:616161510;C:469529175;G:576120961;T:456560109;N:96233", 51, null, null, null, 616161510, 469529175, 576120961, 456560109, 96233, "SRX1898686", "SRS1541536", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.52011, null, 0.38818, null, 0.90193, null, 0.51677, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41151, "SRR3744677", "SRX1898685", "SRS1541535", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto homozygous 4", "GSM2226635", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / ", "moto homozygous 4", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / ", "GSM2226635", "GSM2226635: moto homozygous 4; Danio rerio; ncRNA Seq", "GSM2226635", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226635", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 1771929771.0, 34743721.0, "GSM2226635 r1", "0:51", "A:524609276;C:393148247;G:436902442;T:417188575;N:81231", 51, null, null, null, 524609276, 393148247, 436902442, 417188575, 81231, "SRX1898685", "SRS1541535", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.62874, null, 0.45148, null, 0.89008, null, 0.52837, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41152, "SRR3744676", "SRX1898684", "SRS1541534", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto homozygous 3", "GSM2226634", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / ", "moto homozygous 3", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / ", "GSM2226634", "GSM2226634: moto homozygous 3; Danio rerio; ncRNA Seq", "GSM2226634", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226634", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 1849849917.0, 36271567.0, "GSM2226634 r1", "0:51", "A:554317433;C:408404232;G:459010543;T:428033928;N:83781", 51, null, null, null, 554317433, 408404232, 459010543, 428033928, 83781, "SRX1898684", "SRS1541534", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.69752, null, 0.51829, null, 0.89027, null, 0.53775, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41153, "SRR3744675", "SRX1898683", "SRS1541533", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto homozygous 2", "GSM2226633", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / ", "moto homozygous 2", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / ", "GSM2226633", "GSM2226633: moto homozygous 2; Danio rerio; ncRNA Seq", "GSM2226633", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226633", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 1863615327.0, 36541477.0, "GSM2226633 r1", "0:51", "A:554370010;C:414418365;G:465346091;T:429394630;N:86231", 51, null, null, null, 554370010, 414418365, 465346091, 429394630, 86231, "SRX1898683", "SRS1541533", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.74326, null, 0.52319, null, 0.87361, null, 0.53081, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41154, "SRR3744674", "SRX1898682", "SRS1541532", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto homozygous 1", "GSM2226632", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / ", "moto homozygous 1", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / ", "GSM2226632", "GSM2226632: moto homozygous 1; Danio rerio; ncRNA Seq", "GSM2226632", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226632", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 1453145193.0, 28493043.0, "GSM2226632 r1", "0:51", "A:435644830;C:320413861;G:361678589;T:335340817;N:67096", 51, null, null, null, 435644830, 320413861, 361678589, 335340817, 67096, "SRX1898682", "SRS1541532", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.66367, null, 0.47841, null, 0.88262, null, 0.50114, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41155, "SRR3744673", "SRX1898681", "SRS1541531", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto heterozygous 6", "GSM2226631", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "moto heterozygous 6", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "GSM2226631", "GSM2226631: moto heterozygous 6; Danio rerio; ncRNA Seq", "GSM2226631", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226631", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 2009800248.0, 39407848.0, "GSM2226631 r1", "0:51", "A:586066305;C:443066820;G:503291347;T:477284226;N:91550", 51, null, null, null, 586066305, 443066820, 503291347, 477284226, 91550, "SRX1898681", "SRS1541531", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.69598, null, 0.49191, null, 0.8828, null, 0.51759, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41156, "SRR3744672", "SRX1898680", "SRS1541530", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto heterozygous 5", "GSM2226630", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "moto heterozygous 5", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "GSM2226630", "GSM2226630: moto heterozygous 5; Danio rerio; ncRNA Seq", "GSM2226630", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226630", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 1833618504.0, 35953304.0, "GSM2226630 r1", "0:51", "A:510624241;C:446979639;G:473431335;T:402499572;N:83717", 51, null, null, null, 510624241, 446979639, 473431335, 402499572, 83717, "SRX1898680", "SRS1541530", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.73675, null, 0.50008, null, 0.87957, null, 0.53243, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41157, "SRR3744671", "SRX1898679", "SRS1541529", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto heterozygous 4", "GSM2226629", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "moto heterozygous 4", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "GSM2226629", "GSM2226629: moto heterozygous 4; Danio rerio; ncRNA Seq", "GSM2226629", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226629", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 2011846776.0, 39447976.0, "GSM2226629 r1", "0:51", "A:566935163;C:480777294;G:518987229;T:445055757;N:91333", 51, null, null, null, 566935163, 480777294, 518987229, 445055757, 91333, "SRX1898679", "SRS1541529", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.7246, null, 0.49021, null, 0.88051, null, 0.5202, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41158, "SRR3744670", "SRX1898678", "SRS1541528", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto heterozygous 3", "GSM2226628", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "moto heterozygous 3", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "GSM2226628", "GSM2226628: moto heterozygous 3; Danio rerio; ncRNA Seq", "GSM2226628", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226628", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 1618368312.0, 31732712.0, "GSM2226628 r1", "0:51", "A:476792369;C:353703619;G:406141931;T:381656601;N:73792", 51, null, null, null, 476792369, 353703619, 406141931, 381656601, 73792, "SRX1898678", "SRS1541528", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.67806, null, 0.48273, null, 0.88363, null, 0.53518, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41159, "SRR3744669", "SRX1898677", "SRS1541527", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto heterozygous 2", "GSM2226627", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "moto heterozygous 2", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "GSM2226627", "GSM2226627: moto heterozygous 2; Danio rerio; ncRNA Seq", "GSM2226627", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226627", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 1825076565.0, 35785815.0, "GSM2226627 r1", "0:51", "A:543891854;C:404479103;G:451780092;T:424842227;N:83289", 51, null, null, null, 543891854, 404479103, 451780092, 424842227, 83289, "SRX1898677", "SRS1541527", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.53478, null, 0.39486, null, 0.89899, null, 0.52282, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41160, "SRR3744668", "SRX1898676", "SRS1541526", "SRP077941", "PRJNA327880", "Analysis of piRNA production in meioc moto mutant zebrafish testis", "GSE84060", "Transcriptome Analysis", "We isolated a novel zebrafish mutant denoted meioc moto in which germ cells arrest at the early stage of spermatogonia. The protein encoded by the mutated gene interacts with Piwil1 and affects its intracellular localization. Thus  it is interesting to explore piRNA production in meioc moto mutants. Overall design: Small RNA seq analysis of piRNA production in testes from 6 heterozygous and 5 homozygous moto mutant 10 mpf zebrafish animals.", null, "pubmed:39605693", null, "moto heterozygous 1", "GSM2226626", null, "tissue:testis|strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "moto heterozygous 1", "Sample demultiplexing and FastQ file generation was performed using Casava version 1.8.2. The raw NGS reads in FastQ format were cleaned from partial 3\u2019 adapter sequences using Flexbar v.2.4 using parameters:  m 18  ao 10  as AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Read mapping to the Danio rerio reference genome Zv9/danRer7 build from Illumina iGenomes was carried out using Bowtie v.0.12.8 with parameters:  n 0  e 80  l 18  y   best   nomaqround. All mapped reads in the piRNA range 24 32nt were collected for further analysis with NGSUtils v.0.5.2a and options: bamutils filter  minlen 24  maxlen 32. Transposon annotation for zebrafish DNA  LTR  LINE and SINE elements was derived from the UCSC Table Browser https://genome.ucsc.edu/cgi bin/hgTables   Zv9/danRer7 RepeatMasker track. The 24 32nt reads mapping in sense or antisense orientation to DNA  LTR  LINE and SINE transposon elements 2446490 genomic loci with 967 unique names were summarised per meta feature transposon type using Subread featureCounts v.1.5.0 and options:  M  F SAF  s 1 for sense mapping reads and  M  F SAF  s 2 for antisense mapping reads.  Genome build: Zv9 danRer7 Supplementary files format and content: Tab delimited table with sense  and antisense mapping read counts summarised per transposon type.", "testis", null, "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", null, "strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ ", "GSM2226626", "GSM2226626: moto heterozygous 1; Danio rerio; ncRNA Seq", "GSM2226626", null, "1", "Testes from moto+/  and moto /  zebrafish were removed and total RNA was isolated using Trizol reagent Thermo Fisher Scientific. RNAs smaller than 40nt were isolated using a 15% TBE Urea polyacrylamide gel BioRad  and purified with sodium chloride/isopropanol precipitation. NGS library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina New England BioLabs as recommended by the manufacturer protocol version 2.0 8/13  with 14 PCR cycles for library amplification. The PCR amplified DNA was purified using AMPure XP beads Beckman Coulter. Size selection of the small RNA library was done on LabChip XT instrument Perkin Elmer using a DNA 300 assay kit. The library fractions in the range 120 161 bp were pooled in equal molar ratio. The resulting 2nM pool was denatured and diluted to 10 pM with 5% PhiX spike in DNA and sequenced single read  51 cycles  high output mode on 2 lanes of HiSeq 2000 system Illumina.", "GEO Accession:GSM2226626", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP077941", null, null, null, null, 1358381226.0, 26634926.0, "GSM2226626 r1", "0:51", "A:402110510;C:300618987;G:340178435;T:315410530;N:62764", 51, null, null, null, 402110510, 300618987, 340178435, 315410530, 62764, "SRX1898676", "SRS1541526", "SRA438045", "GEO", "Bioinformatics Core Facility, Institute of Molecular Biology", 1, 0.68106, null, 0.46812, null, 0.87596, null, 0.53427, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2016-07-05", "Adult", "Adult", "Gonad", "Reproductive System"], [41693, "SRR5122167", "SRX2437316", "SRS1872014", "SRP095411", "PRJNA358209", "Identification of a specific 13 miRNA expression signature during follicle activation in Zebrafish", "GSE92639", "Transcriptome Analysis", "Purpose: We aimed to investigate important miRNA events and to define specific miRNA expression signature underlying the follicle activation of zebrafish. Methods: By using small and regular RNA sequencing  we performed transcriptomic analyses of PG primary growth stage I; inactive and PV pre vitellogenic stage II; activated follicles to decipher important miRNA and gene events underlying follicle activation of zebrafish. We identified differentially expressed miRNAs for subsequent qPCR validation and miRNA::target gene prediction. Interaction of candidate miRNA:: target gene pairs were further validated by luciferase reporter assay. Global gene networks involved during PG to PV transition were also assessed by Gene Ontology as well as KEGG pathway analyses. Results and Conclusion: Our expression results indicated that PG follicles can be well differentiated from PV follicles by simply using a specific 13 miRNA expression signature let 7a   7b   7c 5p   7d 5p   7h   7i; miR 21   23a   27c 3p   107a 3p   125b 5p   145 3p   202 5p. Besides  we validated interactions of let 7i::atg4a  miR 202 5p::c23h20orf24 and miR 144::ybx1 by luciferase reporter assay. Purpose: we aimed to investigate important miRNA events and to define specific miRNA expression signature underlying the follicle activation of zebrafish Overall design: To identify differentially expressed miRNAs and its potential downstream targets during follicle activation of zebrafish  we carried out transcriptomic profiling by both small and regular RNA sequencing. By intersecting gene lists of the online predicted targets and RNA seq derived differentially expressed transcripts with a reciprocal expression pattern of miRNAs  we shortlisted 6 pairs of miRNA::target gene for validation using luciferase reporter assay.", null, "pubmed:29228146", null, "PG small RNA seq 2", "GSM2433869", null, "tissue:Ovarian follicle|strain:AB|cell type:Pre vitellogenic follicle|age:from ovary of 3 month zebrafish", "PG small RNA seq 2", "For the RNA seq data  all the pair end reads were mapped to the zebrafish genome  using TopHat version 2.0.11. Genome annotation files with GTF format for known genes were downloaded from Ensembl. FPKM and RPKM values were calculated for each miRNA and gene respectively using Cufflinks software version 2.2.1 with default parameters. Genome build: Zv9 Ensembl release 79 Supplementary files format and content: tab delimited text files include FFKM for each mRNA transcript; tab delimited text files include RFKM for each miRNA.", "Ovarian follicle", "Ovaries from 3 mpf adult zebrafish were dissected in 60% medium of Leibovitz L 15 and follicles PG PV were sorted out according to the size and morphology.", "RNA was extracted with miRNeasy and RNAeasy extraction kits Qiagen RNA Seq libraries were constructed according to Illumima TrueSeq and small RNA seq protocol  and sequenced with the Illumina Hiseq 2000 Single end sequencing and pair end sequencing were used for small RNA seq library and RNA seq library  respectively", "AB fish was housed under a stable flow through condition at 28\u00b0C on a 14L:10D photoperiod with the light on at 0800 and off at 2200. Fish were fed regularly twice a day with live brine shrimp with supplement of commercial tropical fish food at a fixed time basis.", "strain:AB|cell type:Pre vitellogenic follicle|age:from ovary of 3 month zebrafish", "GSM2433869", "GSM2433869: PG small RNA seq 2; Danio rerio; ncRNA Seq", "GSM2433869", null, "1", "RNA was extracted with miRNeasy and RNAeasy extraction kits Qiagen RNA Seq libraries were constructed according to Illumima TrueSeq and small RNA seq protocol  and sequenced with the Illumina Hiseq 2000 Single end sequencing and pair end sequencing were used for small RNA seq library and RNA seq library  respectively", "GEO Accession:GSM2433869", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095411", null, null, "Ctrl_PV_1.fq.gz", "fastq", 532189753.0, 19043107.0, "GSM2433869 r1", "0:27.95 1:0", "A:138460901;C:107807428;G:115489810;T:170431567;N:47", 27, 0, null, null, 138460901, 107807428, 115489810, 170431567, 47, "SRX2437316", "SRS1872014", "SRA505873", "GEO", "Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Health", 1, 0.86612, null, 0.65562, null, 0.84486, null, 0.53167, null, 26, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-12-20", "Adult", "Adult", "Gonad", "Reproductive System"], [41694, "SRR5122166", "SRX2437315", "SRS1872013", "SRP095411", "PRJNA358209", "Identification of a specific 13 miRNA expression signature during follicle activation in Zebrafish", "GSE92639", "Transcriptome Analysis", "Purpose: We aimed to investigate important miRNA events and to define specific miRNA expression signature underlying the follicle activation of zebrafish. Methods: By using small and regular RNA sequencing  we performed transcriptomic analyses of PG primary growth stage I; inactive and PV pre vitellogenic stage II; activated follicles to decipher important miRNA and gene events underlying follicle activation of zebrafish. We identified differentially expressed miRNAs for subsequent qPCR validation and miRNA::target gene prediction. Interaction of candidate miRNA:: target gene pairs were further validated by luciferase reporter assay. Global gene networks involved during PG to PV transition were also assessed by Gene Ontology as well as KEGG pathway analyses. Results and Conclusion: Our expression results indicated that PG follicles can be well differentiated from PV follicles by simply using a specific 13 miRNA expression signature let 7a   7b   7c 5p   7d 5p   7h   7i; miR 21   23a   27c 3p   107a 3p   125b 5p   145 3p   202 5p. Besides  we validated interactions of let 7i::atg4a  miR 202 5p::c23h20orf24 and miR 144::ybx1 by luciferase reporter assay. Purpose: we aimed to investigate important miRNA events and to define specific miRNA expression signature underlying the follicle activation of zebrafish Overall design: To identify differentially expressed miRNAs and its potential downstream targets during follicle activation of zebrafish  we carried out transcriptomic profiling by both small and regular RNA sequencing. By intersecting gene lists of the online predicted targets and RNA seq derived differentially expressed transcripts with a reciprocal expression pattern of miRNAs  we shortlisted 6 pairs of miRNA::target gene for validation using luciferase reporter assay.", null, "pubmed:29228146", null, "PG small RNA seq 1", "GSM2433868", null, "tissue:Ovarian follicle|strain:AB|cell type:Primary growth follicle|age:from ovary of 3 month zebrafish", "PG small RNA seq 1", "For the RNA seq data  all the pair end reads were mapped to the zebrafish genome  using TopHat version 2.0.11. Genome annotation files with GTF format for known genes were downloaded from Ensembl. FPKM and RPKM values were calculated for each miRNA and gene respectively using Cufflinks software version 2.2.1 with default parameters. Genome build: Zv9 Ensembl release 79 Supplementary files format and content: tab delimited text files include FFKM for each mRNA transcript; tab delimited text files include RFKM for each miRNA.", "Ovarian follicle", "Ovaries from 3 mpf adult zebrafish were dissected in 60% medium of Leibovitz L 15 and follicles PG PV were sorted out according to the size and morphology.", "RNA was extracted with miRNeasy and RNAeasy extraction kits Qiagen RNA Seq libraries were constructed according to Illumima TrueSeq and small RNA seq protocol  and sequenced with the Illumina Hiseq 2000 Single end sequencing and pair end sequencing were used for small RNA seq library and RNA seq library  respectively", "AB fish was housed under a stable flow through condition at 28\u00b0C on a 14L:10D photoperiod with the light on at 0800 and off at 2200. Fish were fed regularly twice a day with live brine shrimp with supplement of commercial tropical fish food at a fixed time basis.", "strain:AB|cell type:Primary growth follicle|age:from ovary of 3 month zebrafish", "GSM2433868", "GSM2433868: PG small RNA seq 1; Danio rerio; ncRNA Seq", "GSM2433868", null, "1", "RNA was extracted with miRNeasy and RNAeasy extraction kits Qiagen RNA Seq libraries were constructed according to Illumima TrueSeq and small RNA seq protocol  and sequenced with the Illumina Hiseq 2000 Single end sequencing and pair end sequencing were used for small RNA seq library and RNA seq library  respectively", "GEO Accession:GSM2433868", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP095411", null, null, "Ctrl_PG_1.fq.gz", "fastq", 368945203.0, 13147324.0, "GSM2433868 r1", "0:28.06 1:0", "A:96466912;C:75527992;G:78177838;T:118772423;N:38", 28, 0, null, null, 96466912, 75527992, 78177838, 118772423, 38, "SRX2437315", "SRS1872013", "SRA505873", "GEO", "Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Health", 1, 0.8524, null, 0.67638, null, 0.86074, null, 0.48958, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-12-20", "Adult", "Adult", "Gonad", "Reproductive System"], [44967, "SRR6345660", "SRX3442976", "SRS2733636", "SRP126106", "PRJNA421016", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [small RNA]", "GSE107682", "Transcriptome Analysis", "Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Zebrafish were grown under standard conditions. Total ovary or size selected Oocytes were used to extact RNA from het of tdrd6a mutant fish.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "smRNA seq library of ovary from tdrd6a mut fish", "GSM2875719", null, "source name:Ovary from tdrd6a mut fish|tissue:whole ovary|genotype:tdrd6a mutant", "smRNA seq library of ovary from tdrd6a mut fish", "1. Adapter trimming with cutadapt  O 8  m 26  M 38  a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 2. Low quality read filtering with fastq quality filter   q 20  p 100  Q 33. 3. Duplicate reads were collapsed using the unique molecule identifiers UMIs added during library preparation 4 random bases at both the five prime and three prime end  using a custom bash script. 4. UMIs were trimmed with seqtk trimfq  b 4  a 4 5. Reads with less than 15 nt in length were filtered out with seqtk seq  L 15\u00a0 6. Mapping was done to Zebrafish  Danio rerio  genome assembly Zv9 with bowtie v0.12.8   tryhard   best   strata   chunkmbs 256  v 1  M 5. 7. Bigwig tracks normalized to the number of mapped reads were created using genomeCoverageBed  bg  split  scale bedtools 2.25.0 followed by bedGraphToBigWig Kent utilities.\u00a0 \u00a0 8. Mapped reads converted to bed with bamToBed where intersected with the locations of transposable elements LINE  SINE  LTR and DNA downloaded from the UCSC genome browser repeat masker track  Zv9 using bedtools intersect  a reads  b transposons  wa  wb  bed  f 1.0  nonamecheck to keep both the read and the transposon information. The arguments  s/ S were also set to find reads mapping sense or antisense to the transposons. Results are in data file transposons counts.txt.gz Genome build: Zv9 Supplementary files format and content: transposons counts.txt.gz is a compressed tab delimited file. Each line corresponds a read that overlaps and annotated transposon. The fields chr re  start re  end re  repFamily  repName strand re  and repClass represent the location and classification of the repeat elements as described in the RepeatMasker track of UCSC. Feature is whether they are DNA or RNA transposons  and readlength the length of the read that. Sample is the sample name  and Mapping whether teh reads mapped sense or antisense in relation to the transposon it maps to.\u00a0 Supplementary files format and content: Files ending in .bw are bigwig tracks.", "Ovary from tdrd6a mut fish", null, "RNA was extracted from ovary tissue  as indicated  by Trizol extraction. Standard smRNA seq library preperation", null, "tissue:whole ovary|genotype:tdrd6a mutant", "GSM2875719", "GSM2875719: smRNA seq library of ovary from tdrd6a mut fish; Danio rerio; ncRNA Seq", "GSM2875719", null, "1", "RNA was extracted from ovary tissue  as indicated  by Trizol extraction. Standard smRNA seq library preperation", "GEO Accession:GSM2875719", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP126106", null, null, "Tdrd6a-mut-ovary-input-Adult.fastq.gz", "fastq", 817885062.0, 16036962.0, "GSM2875719 r1", "0:51", "A:212456064;C:163491733;G:233627239;T:208262707;N:47319", 51, null, null, null, 212456064, 163491733, 233627239, 208262707, 47319, "SRX3442976", "SRS2733636", "SRA636010", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.46308, null, 0.13668, null, 0.83587, null, 0.79104, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2017-12-04", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [44968, "SRR6345659", "SRX3442975", "SRS2733637", "SRP126106", "PRJNA421016", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [small RNA]", "GSE107682", "Transcriptome Analysis", "Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: Zebrafish were grown under standard conditions. Total ovary or size selected Oocytes were used to extact RNA from het of tdrd6a mutant fish.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "smRNA seq library of ovary from tdrd6a het fish", "GSM2875718", null, "source name:Ovary from tdrd6a het fish|tissue:whole ovary|genotype:tdrd6a heterozygous", "smRNA seq library of ovary from tdrd6a het fish", "1. Adapter trimming with cutadapt  O 8  m 26  M 38  a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 2. Low quality read filtering with fastq quality filter   q 20  p 100  Q 33. 3. Duplicate reads were collapsed using the unique molecule identifiers UMIs added during library preparation 4 random bases at both the five prime and three prime end  using a custom bash script. 4. UMIs were trimmed with seqtk trimfq  b 4  a 4 5. Reads with less than 15 nt in length were filtered out with seqtk seq  L 15\u00a0 6. Mapping was done to Zebrafish  Danio rerio  genome assembly Zv9 with bowtie v0.12.8   tryhard   best   strata   chunkmbs 256  v 1  M 5. 7. Bigwig tracks normalized to the number of mapped reads were created using genomeCoverageBed  bg  split  scale bedtools 2.25.0 followed by bedGraphToBigWig Kent utilities.\u00a0 \u00a0 8. Mapped reads converted to bed with bamToBed where intersected with the locations of transposable elements LINE  SINE  LTR and DNA downloaded from the UCSC genome browser repeat masker track  Zv9 using bedtools intersect  a reads  b transposons  wa  wb  bed  f 1.0  nonamecheck to keep both the read and the transposon information. The arguments  s/ S were also set to find reads mapping sense or antisense to the transposons. Results are in data file transposons counts.txt.gz Genome build: Zv9 Supplementary files format and content: transposons counts.txt.gz is a compressed tab delimited file. Each line corresponds a read that overlaps and annotated transposon. The fields chr re  start re  end re  repFamily  repName strand re  and repClass represent the location and classification of the repeat elements as described in the RepeatMasker track of UCSC. Feature is whether they are DNA or RNA transposons  and readlength the length of the read that. Sample is the sample name  and Mapping whether teh reads mapped sense or antisense in relation to the transposon it maps to.\u00a0 Supplementary files format and content: Files ending in .bw are bigwig tracks.", "Ovary from tdrd6a het fish", null, "RNA was extracted from ovary tissue  as indicated  by Trizol extraction. Standard smRNA seq library preperation", null, "tissue:whole ovary|genotype:tdrd6a heterozygous", "GSM2875718", "GSM2875718: smRNA seq library of ovary from tdrd6a het fish; Danio rerio; ncRNA Seq", "GSM2875718", null, "1", "RNA was extracted from ovary tissue  as indicated  by Trizol extraction. Standard smRNA seq library preperation", "GEO Accession:GSM2875718", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP126106", null, null, "Tdrd6a-het-ovary-input-Adult.fastq.gz", "fastq", 1452353571.0, 28477521.0, "GSM2875718 r1", "0:51", "A:397993735;C:284194126;G:396142390;T:373939235;N:84085", 51, null, null, null, 397993735, 284194126, 396142390, 373939235, 84085, "SRX3442975", "SRS2733637", "SRA636010", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.3869, null, 0.1369, null, 0.86397, null, 0.77165, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2017-12-04", "Undetermined", "Undetermined", "Gonad", "Reproductive System"], [68556, "SRR18028171", "SRX14182301", "SRS12005942", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "6WT 3", null, "strain:AB|isolate:replicate3|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "wt 3 S11 L001 R1", "011", "011", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "wt-3_S11_L001_R1_001.fastq.gz wt-3_S11_L001_R2_001.fastq.gz", "fastq fastq", 3576981600.0, 11923272.0, "wt 3 S11 L001 R1 001.fastq.gz", "0:150 1:150", "A:689001630;C:496844981;G:1779990511;T:610974133;N:170345", 150, 150, null, null, 689001630, 496844981, 1779990511, 610974133, 170345, "SRX14182301", "SRS12005942", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.8179, 0.81697, 0.60905, 0.60864, 0.82692, 0.82915, 0.52425, 0.52623, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [68557, "SRR18028172", "SRX14182300", "SRS12005941", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "5WT 2", null, "strain:AB|isolate:replicate2|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "wt 2 S10 L001 R1", "009", "009", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "wt-2_S10_L001_R1_001.fastq.gz wt-2_S10_L001_R2_001.fastq.gz", "fastq fastq", 4200013800.0, 14000046.0, "wt 2 S10 L001 R1 001.fastq.gz", "0:150 1:150", "A:781057232;C:617020885;G:2110010128;T:691723797;N:201758", 150, 150, null, null, 781057232, 617020885, 2110010128, 691723797, 201758, "SRX14182300", "SRS12005941", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.8213, 0.82216, 0.59414, 0.59507, 0.81089, 0.81306, 0.53839, 0.52755, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [68558, "SRR18028173", "SRX14182299", "SRS12005940", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "4WT 1", null, "strain:AB|isolate:replicate1|ecotype:wt|age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "wt 1 S9 L001 R1", "007", "007", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "wt-1_S9_L001_R1_001.fastq.gz wt-1_S9_L001_R2_001.fastq.gz", "fastq fastq", 4820063700.0, 16066879.0, "wt 1 S9 L001 R1 001.fastq.gz", "0:150 1:150", "A:996304548;C:657334691;G:2379519106;T:786675131;N:230224", 150, 150, null, null, 996304548, 657334691, 2379519106, 786675131, 230224, "SRX14182299", "SRS12005940", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.80219, 0.80319, 0.60906, 0.60878, 0.83238, 0.83303, 0.52559, 0.51852, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [68559, "SRR18028174", "SRX14182298", "SRS12005939", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "3PLD6 3", null, "strain:AB|isolate:replicate3|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "pld6 3 S3 L003 R1", "005", "005", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "pld6-3_S3_L003_R1_001.fastq.gz pld6-3_S3_L003_R2_001.fastq.gz", "fastq fastq", 816686700.0, 2722289.0, "pld6 3 S3 L003 R1 001.fastq.gz", "0:150 1:150", "A:145681738;C:137123477;G:401610833;T:132256312;N:14340", 150, 150, null, null, 145681738, 137123477, 401610833, 132256312, 14340, "SRX14182298", "SRS12005939", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.78314, 0.73942, 0.07641, 0.09097, 0.91603, 0.91545, 0.6312, 0.64467, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [68560, "SRR18028175", "SRX14182297", "SRS12005938", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "2PLD6 2", null, "strain:AB|isolate:replicate2|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "pld6 2 S2 L003 R1", "003", "003", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "pld6-2_S2_L003_R1_001.fastq.gz pld6-2_S2_L003_R2_001.fastq.gz", "fastq fastq", 6546276900.0, 21820923.0, "pld6 2 S2 L003 R1 001.fastq.gz", "0:150 1:150", "A:1161502458;C:1095580994;G:3226725392;T:1062358099;N:109957", 150, 150, null, null, 1161502458, 1095580994, 3226725392, 1062358099, 109957, "SRX14182297", "SRS12005938", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.6471, 0.593, 0.07935, 0.09168, 0.92058, 0.92005, 0.53626, 0.65284, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"], [68561, "SRR18028176", "SRX14182296", "SRS12005937", "SRP359829", "PRJNA807002", "samll RNA seq of zebrafish gonads of wildtype and pld6 /  at 22 dpf", "PRJNA807002", "Other", "In this study  we generated zebrafish pld6 knockouts and found that the pld6 null mutants developed as infertile males  with testes containing no germ cells. Pld6 is considered to be a candidate ribonuclease participating in primary piRNA biogenesis which is essential for the survival of germ cells. We deep sequenced 20 33 nt total small RNAs obtained from 22 dpf wildtype and pld6 /  gonad with three repetition. In pld6 /  gonad  small RNAs mapped to the known piRNA clusters were almost absent. Moreover  piRNA clusters in pld6 /  gonad lost the enrichment for uridine at the first position or for adenine at the 10th position. our results unequivocally demonstrate a conserved role for MitoPLD in the piRNA biogenesis pathway.", null, null, null, null, "1PLD6 1", null, "strain:AB|isolate:replicate1|ecotype:pld6 / |age:post fertilization day 22|dev stage:juvenile|sex:missing|tissue:Gonad|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "pld6 1 S1 L003 R1", "001", "001", "Zebrafish larvae were anesthetized in 0.2 mg/mL MS 222 and disected to isolate gonads under a microscope. Three wildtype or mutant gonads were mixed into one repeat  and three repeats  were performed for samll RNA sequencing.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP359829", null, null, "pld6-1_S1_L003_R1_001.fastq.gz pld6-1_S1_L003_R2_001.fastq.gz", "fastq fastq", 5535130200.0, 18450434.0, "pld6 1 S1 L003 R1 001.fastq.gz", "0:150 1:150", "A:1014761790;C:833992394;G:2813863824;T:872418512;N:93680", 150, 150, null, null, 1014761790, 833992394, 2813863824, 872418512, 93680, "SRX14182296", "SRS12005937", "SRA1372890", "Huazhong agricultural university|School of Life Science and Technology", "Huazhong agricultural university", 2, 0.70358, 0.73288, 0.08649, 0.09366, 0.91066, 0.90914, 0.6197, 0.6207, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-02-14", "Multi-stage", "Multi-stage", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 21, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [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 from run_metadata where \"experiment.library_source\" = :p0 and \"experiment.library_strategy\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC", "p1": "ncRNA-Seq", "p2": "Gonad"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "results": [{"value": "ncRNA-Seq", "label": "ncRNA-Seq", "count": 21, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&tissue_curation=Gonad", "selected": true}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 21, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "selected": true}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "results": [{"value": "size fractionation", "label": "size fractionation", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&experiment.library_selection=size+fractionation", "selected": false}, {"value": "other", "label": "other", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&experiment.library_selection=other", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 21, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "results": [{"value": "Adult", "label": "Adult", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&devstage_curation_coarse=Adult", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&devstage_curation_coarse=Multi-stage", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&devstage_curation_coarse=Undetermined", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "results": [{"value": "Adult", "label": "Adult", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&devstage_curation=Adult", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&devstage_curation=Multi-stage", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&devstage_curation=Undetermined", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "results": [{"value": "Reproductive System", "label": "Reproductive System", "count": 21, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&tissue_curation_coarse=Reproductive+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "results": [{"value": "Gonad", "label": "Gonad", "count": 21, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad", "results": [{"value": "unknown", "label": "unknown", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&technology=unknown", "selected": false}, {"value": "generic-scrnaseq-only", "label": "generic-scrnaseq-only", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&experiment.library_strategy=ncRNA-Seq&tissue_curation=Gonad&technology=generic-scrnaseq-only", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 115.13043599916273}