RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

69 rows where devstage_curation = "Adult" and experiment.library_strategy = "ncRNA-Seq"

✎ View and edit SQL

This data as json, CSV (advanced)

tissue_curation 4

technology 1

experiment.platform 1

experiment.library_strategy 1

  • ncRNA-Seq · 69 ✖

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Adult · 69 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
41150 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.   pubmed:39605693   moto homozygous 5 GSM2226636   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / GSM2226636 GSM2226636: moto homozygous 5; Danio rerio; ncRNA Seq GSM2226636   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   SRP077941         2118467988.0 41538588.0 GSM2226636 r1 0:51 A:616161510;C:469529175;G:576120961;T:456560109;N:96233 51       616161510 469529175 576120961 456560109 96233 SRX1898686 SRS1541536 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.52011   0.38818   0.90193   0.51677   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41151 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.   pubmed:39605693   moto homozygous 4 GSM2226635   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / GSM2226635 GSM2226635: moto homozygous 4; Danio rerio; ncRNA Seq GSM2226635   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   SRP077941         1771929771.0 34743721.0 GSM2226635 r1 0:51 A:524609276;C:393148247;G:436902442;T:417188575;N:81231 51       524609276 393148247 436902442 417188575 81231 SRX1898685 SRS1541535 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.62874   0.45148   0.89008   0.52837   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41152 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.   pubmed:39605693   moto homozygous 3 GSM2226634   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / GSM2226634 GSM2226634: moto homozygous 3; Danio rerio; ncRNA Seq GSM2226634   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   SRP077941         1849849917.0 36271567.0 GSM2226634 r1 0:51 A:554317433;C:408404232;G:459010543;T:428033928;N:83781 51       554317433 408404232 459010543 428033928 83781 SRX1898684 SRS1541534 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.69752   0.51829   0.89027   0.53775   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41153 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.   pubmed:39605693   moto homozygous 2 GSM2226633   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / GSM2226633 GSM2226633: moto homozygous 2; Danio rerio; ncRNA Seq GSM2226633   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   SRP077941         1863615327.0 36541477.0 GSM2226633 r1 0:51 A:554370010;C:414418365;G:465346091;T:429394630;N:86231 51       554370010 414418365 465346091 429394630 86231 SRX1898683 SRS1541533 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.74326   0.52319   0.87361   0.53081   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41154 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.   pubmed:39605693   moto homozygous 1 GSM2226632   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:homozygous mutant moto / GSM2226632 GSM2226632: moto homozygous 1; Danio rerio; ncRNA Seq GSM2226632   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   SRP077941         1453145193.0 28493043.0 GSM2226632 r1 0:51 A:435644830;C:320413861;G:361678589;T:335340817;N:67096 51       435644830 320413861 361678589 335340817 67096 SRX1898682 SRS1541532 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.66367   0.47841   0.88262   0.50114   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41155 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.   pubmed:39605693   moto heterozygous 6 GSM2226631   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ GSM2226631 GSM2226631: moto heterozygous 6; Danio rerio; ncRNA Seq GSM2226631   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   SRP077941         2009800248.0 39407848.0 GSM2226631 r1 0:51 A:586066305;C:443066820;G:503291347;T:477284226;N:91550 51       586066305 443066820 503291347 477284226 91550 SRX1898681 SRS1541531 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.69598   0.49191   0.8828   0.51759   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41156 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.   pubmed:39605693   moto heterozygous 5 GSM2226630   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ GSM2226630 GSM2226630: moto heterozygous 5; Danio rerio; ncRNA Seq GSM2226630   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   SRP077941         1833618504.0 35953304.0 GSM2226630 r1 0:51 A:510624241;C:446979639;G:473431335;T:402499572;N:83717 51       510624241 446979639 473431335 402499572 83717 SRX1898680 SRS1541530 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.73675   0.50008   0.87957   0.53243   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41157 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.   pubmed:39605693   moto heterozygous 4 GSM2226629   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ GSM2226629 GSM2226629: moto heterozygous 4; Danio rerio; ncRNA Seq GSM2226629   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   SRP077941         2011846776.0 39447976.0 GSM2226629 r1 0:51 A:566935163;C:480777294;G:518987229;T:445055757;N:91333 51       566935163 480777294 518987229 445055757 91333 SRX1898679 SRS1541529 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.7246   0.49021   0.88051   0.5202   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41158 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.   pubmed:39605693   moto heterozygous 3 GSM2226628   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ GSM2226628 GSM2226628: moto heterozygous 3; Danio rerio; ncRNA Seq GSM2226628   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   SRP077941         1618368312.0 31732712.0 GSM2226628 r1 0:51 A:476792369;C:353703619;G:406141931;T:381656601;N:73792 51       476792369 353703619 406141931 381656601 73792 SRX1898678 SRS1541528 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.67806   0.48273   0.88363   0.53518   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41159 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.   pubmed:39605693   moto heterozygous 2 GSM2226627   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ GSM2226627 GSM2226627: moto heterozygous 2; Danio rerio; ncRNA Seq GSM2226627   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   SRP077941         1825076565.0 35785815.0 GSM2226627 r1 0:51 A:543891854;C:404479103;G:451780092;T:424842227;N:83289 51       543891854 404479103 451780092 424842227 83289 SRX1898677 SRS1541527 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.53478   0.39486   0.89899   0.52282   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41160 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.   pubmed:39605693   moto heterozygous 1 GSM2226626   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’ 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   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.   strain:Tuebingen/WIK|age:10 month|genotype:heterozygous mutant moto+/ GSM2226626 GSM2226626: moto heterozygous 1; Danio rerio; ncRNA Seq GSM2226626   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   SRP077941         1358381226.0 26634926.0 GSM2226626 r1 0:51 A:402110510;C:300618987;G:340178435;T:315410530;N:62764 51       402110510 300618987 340178435 315410530 62764 SRX1898676 SRS1541526 SRA438045 GEO Bioinformatics Core Facility, Institute of Molecular Biology 1 0.68106   0.46812   0.87596   0.53427   51   B   usable mapping rate illumina hiseq_era unknown size_fractionation nebnext bulk unknown unknown   Germany 2016-07-05 Adult Adult Gonad Reproductive System
41693 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.   pubmed:29228146   PG small RNA seq 2 GSM2433869   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°C 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   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   SRP095411     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     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   0.65562   0.84486   0.53167   26   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   United States 2016-12-20 Adult Adult Gonad Reproductive System
41694 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.   pubmed:29228146   PG small RNA seq 1 GSM2433868   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°C 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   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   SRP095411     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     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   0.67638   0.86074   0.48958   27   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   United States 2016-12-20 Adult Adult Gonad Reproductive System
48990 48990 SRR7612999 SRX4477699 SRS3602899 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 156 ZF brain smallRNAseq GSM3309607   source name:brain|strain:AB JxT\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male NH FLI 156 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male GSM3309607 GSM3309607: NH FLI 156 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309607   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309607 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         681376400.0 13627528.0 GSM3309607 r1 0:50 A:149742268;C:163827889;G:200725169;T:167045618;N:35456 50       149742268 163827889 200725169 167045618 35456 SRX4477699 SRS3602899 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00576   0.00087   0.9959   0.70299   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48991 48991 SRR7612998 SRX4477698 SRS3602898 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 154 ZF brain smallRNAseq GSM3309606   source name:brain|strain:AB JxT\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male NH FLI 154 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male GSM3309606 GSM3309606: NH FLI 154 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309606   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309606 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1196666100.0 23933322.0 GSM3309606 r1 0:50 A:243243770;C:320296221;G:371488432;T:261584801;N:52876 50       243243770 320296221 371488432 261584801 52876 SRX4477698 SRS3602898 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01627   0.00325   0.99293   0.7183   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48992 48992 SRR7612997 SRX4477697 SRS3602897 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 153 ZF brain smallRNAseq GSM3309605   source name:brain|strain:AB JxT\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male NH FLI 153 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male GSM3309605 GSM3309605: NH FLI 153 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309605   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309605 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         2123002650.0 42460053.0 GSM3309605 r1 0:50 A:461619025;C:513713514;G:623358074;T:524212056;N:99981 50       461619025 513713514 623358074 524212056 99981 SRX4477697 SRS3602897 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02759   0.00329   0.99287   0.62418   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48993 48993 SRR7612996 SRX4477696 SRS3602896 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 152 ZF brain smallRNAseq GSM3309604   source name:brain|strain:AB JxT\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male NH FLI 152 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male GSM3309604 GSM3309604: NH FLI 152 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309604   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309604 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1434455750.0 28689115.0 GSM3309604 r1 0:50 A:283488481;C:381046485;G:446805516;T:323062667;N:52601 50       283488481 381046485 446805516 323062667 52601 SRX4477696 SRS3602896 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.04109   0.00889   0.98786   0.73333   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48994 48994 SRR7612995 SRX4477695 SRS3602895 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 150 ZF brain smallRNAseq GSM3309603   source name:brain|strain:AB JxT\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male NH FLI 150 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:brain|age:3 years|Sex:male GSM3309603 GSM3309603: NH FLI 150 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309603   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309603 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1338770950.0 26775419.0 GSM3309603 r1 0:50 A:269497925;C:353627074;G:405585207;T:310020028;N:40716 50       269497925 353627074 405585207 310020028 40716 SRX4477695 SRS3602895 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02887   0.00518   0.99052   0.68568   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48995 48995 SRR7612994 SRX4477694 SRS3602894 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 143 ZF brain smallRNAseq GSM3309602   source name:brain|strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male NH FLI 143 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male GSM3309602 GSM3309602: NH FLI 143 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309602   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309602 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         626017200.0 12520344.0 GSM3309602 r1 0:50 A:134906441;C:152023722;G:185947594;T:153106683;N:32760 50       134906441 152023722 185947594 153106683 32760 SRX4477694 SRS3602894 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00695   0.00127   0.99529   0.71945   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48996 48996 SRR7612993 SRX4477693 SRS3602893 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 142 ZF brain smallRNAseq GSM3309601   source name:brain|strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male NH FLI 142 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male GSM3309601 GSM3309601: NH FLI 142 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309601   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309601 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         602153350.0 12043067.0 GSM3309601 r1 0:50 A:130038217;C:144346274;G:180485776;T:147255994;N:27089 50       130038217 144346274 180485776 147255994 27089 SRX4477693 SRS3602893 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01383   0.002   0.99545   0.61426   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48997 48997 SRR7612992 SRX4477692 SRS3602892 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 140 ZF brain smallRNAseq GSM3309600   source name:brain|strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male NH FLI 140 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male GSM3309600 GSM3309600: NH FLI 140 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309600   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309600 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1040923600.0 20818472.0 GSM3309600 r1 0:50 A:226013762;C:247845507;G:308453469;T:258569100;N:41762 50       226013762 247845507 308453469 258569100 41762 SRX4477692 SRS3602892 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01433   0.00292   0.99484   0.60865   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48998 48998 SRR7612991 SRX4477691 SRS3602891 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 139 ZF brain smallRNAseq GSM3309599   source name:brain|strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male NH FLI 139 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male GSM3309599 GSM3309599: NH FLI 139 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309599   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309599 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         612192100.0 12243842.0 GSM3309599 r1 0:50 A:133152501;C:147001376;G:181291514;T:150727221;N:19488 50       133152501 147001376 181291514 150727221 19488 SRX4477691 SRS3602891 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01776   0.00244   0.9945   0.59354   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
48999 48999 SRR7612990 SRX4477690 SRS3602890 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 138 ZF brain smallRNAseq GSM3309598   source name:brain|strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male NH FLI 138 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:brain|age:2 years|Sex:male GSM3309598 GSM3309598: NH FLI 138 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309598   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309598 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1205010900.0 24100218.0 GSM3309598 r1 0:50 A:254443623;C:292846390;G:362958072;T:294704148;N:58667 50       254443623 292846390 362958072 294704148 58667 SRX4477690 SRS3602890 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02329   0.00277   0.99442   0.57362   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49000 49000 SRR7612989 SRX4477689 SRS3602889 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 129 ZF brain smallRNAseq GSM3309597   source name:brain|strain:AB JxT\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male NH FLI 129 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male GSM3309597 GSM3309597: NH FLI 129 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309597   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309597 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         905166650.0 18103333.0 GSM3309597 r1 0:50 A:183798257;C:231083843;G:277164667;T:213076607;N:43276 50       183798257 231083843 277164667 213076607 43276 SRX4477689 SRS3602889 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03359   0.00484   0.99105   0.62836   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49001 49001 SRR7612988 SRX4477688 SRS3602888 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 128 ZF brain smallRNAseq GSM3309596   source name:brain|strain:AB JxT\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male NH FLI 128 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male GSM3309596 GSM3309596: NH FLI 128 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309596   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309596 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1304729150.0 26094583.0 GSM3309596 r1 0:50 A:261793442;C:350134689;G:395019822;T:297741148;N:40049 50       261793442 350134689 395019822 297741148 40049 SRX4477688 SRS3602888 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02649   0.00457   0.99038   0.65849   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49002 49002 SRR7612987 SRX4477687 SRS3602887 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 127 ZF brain smallRNAseq GSM3309595   source name:brain|strain:AB JxT\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male NH FLI 127 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male GSM3309595 GSM3309595: NH FLI 127 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309595   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309595 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1087717850.0 21754357.0 GSM3309595 r1 0:50 A:233191242;C:266842531;G:322704369;T:264927170;N:52538 50       233191242 266842531 322704369 264927170 52538 SRX4477687 SRS3602887 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02888   0.00371   0.99322   0.60352   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49003 49003 SRR7612986 SRX4477686 SRS3602886 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 125 ZF brain smallRNAseq GSM3309594   source name:brain|strain:AB JxT\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male NH FLI 125 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male GSM3309594 GSM3309594: NH FLI 125 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309594   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309594 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         745015250.0 14900305.0 GSM3309594 r1 0:50 A:160725228;C:177900490;G:219158125;T:187195853;N:35554 50       160725228 177900490 219158125 187195853 35554 SRX4477686 SRS3602886 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02669   0.00263   0.99348   0.564   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49004 49004 SRR7612985 SRX4477685 SRS3602885 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 124 ZF brain smallRNAseq GSM3309593   source name:brain|strain:AB JxT\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male NH FLI 124 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:brain|age:1 year|Sex:male GSM3309593 GSM3309593: NH FLI 124 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309593   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309593 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1305373550.0 26107471.0 GSM3309593 r1 0:50 A:303613747;C:302726844;G:364736102;T:334233710;N:63147 50       303613747 302726844 364736102 334233710 63147 SRX4477685 SRS3602885 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03499   0.00371   0.99362   0.5891   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49005 49005 SRR7612984 SRX4477684 SRS3602884 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 114 ZF brain smallRNAseq GSM3309592   source name:brain|strain:AB JxT\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male NH FLI 114 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male GSM3309592 GSM3309592: NH FLI 114 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309592   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309592 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         722165700.0 14443314.0 GSM3309592 r1 0:50 A:158514262;C:171787722;G:214687494;T:177143548;N:32674 50       158514262 171787722 214687494 177143548 32674 SRX4477684 SRS3602884 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01251   0.00195   0.99584   0.60892   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49006 49006 SRR7612983 SRX4477683 SRS3602883 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 109 ZF brain smallRNAseq GSM3309591   source name:brain|strain:AB JxT\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male NH FLI 109 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male GSM3309591 GSM3309591: NH FLI 109 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309591   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309591 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1295539450.0 25910789.0 GSM3309591 r1 0:50 A:292712777;C:309650541;G:373811139;T:319271810;N:93183 50       292712777 309650541 373811139 319271810 93183 SRX4477683 SRS3602883 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.07779   0.00531   0.99431   0.5455   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49007 49007 SRR7612982 SRX4477682 SRS3602882 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 99 100 ZF brain smallRNAseq GSM3309590   source name:brain|strain:AB JxT\xFC|tissue:brain|age:6 month|Sex:male NH FLI 99 100 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:brain|age:6 month|Sex:male GSM3309590 GSM3309590: NH FLI 99 100 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309590   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309590 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         433373950.0 8667479.0 GSM3309590 r1 0:50 A:93001141;C:105441767;G:129717150;T:105194380;N:19512 50       93001141 105441767 129717150 105194380 19512 SRX4477682 SRS3602882 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01476   0.0021   0.99555   0.64442   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49008 49008 SRR7612981 SRX4477681 SRS3602881 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 97 98 ZF brain smallRNAseq GSM3309589   source name:brain|strain:AB JxT\xFC|tissue:brain|age:6 month|Sex:male NH FLI 97 98 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:brain|age:6 month|Sex:male GSM3309589 GSM3309589: NH FLI 97 98 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309589   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309589 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         510617150.0 10212343.0 GSM3309589 r1 0:50 A:110447838;C:121736402;G:152183388;T:126228958;N:20564 50       110447838 121736402 152183388 126228958 20564 SRX4477681 SRS3602881 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01519   0.00277   0.99409   0.63157   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49009 49009 SRR7612980 SRX4477680 SRS3602880 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 95 96 ZF brain smallRNAseq GSM3309588   source name:brain|strain:AB JxT\xFC|tissue:brain|age:6 month|Sex:male NH FLI 95 96 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:brain|age:6 month|Sex:male GSM3309588 GSM3309588: NH FLI 95 96 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309588   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309588 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         472516100.0 9450322.0 GSM3309588 r1 0:50 A:103765011;C:113400404;G:139267589;T:116067916;N:15180 50       103765011 113400404 139267589 116067916 15180 SRX4477680 SRS3602880 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01894   0.00292   0.99411   0.58808   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49010 49010 SRR7612979 SRX4477679 SRS3602879 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 116 ZF brain smallRNAseq GSM3309587   source name:brain|strain:AB JxT\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male NH FLI 116 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male GSM3309587 GSM3309587: NH FLI 116 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309587   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309587 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         715226800.0 14304536.0 GSM3309587 r1 0:50 A:159838696;C:168777427;G:208871390;T:177701320;N:37967 50       159838696 168777427 208871390 177701320 37967 SRX4477679 SRS3602879 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00535   0.00095   0.99677   0.70896   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49011 49011 SRR7612978 SRX4477678 SRS3602878 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 112 ZF brain smallRNAseq GSM3309586   source name:brain|strain:AB JxT\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male NH FLI 112 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male GSM3309586 GSM3309586: NH FLI 112 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309586   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309586 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1026870700.0 20537414.0 GSM3309586 r1 0:50 A:221725135;C:249408204;G:304663061;T:251034143;N:40157 50       221725135 249408204 304663061 251034143 40157 SRX4477678 SRS3602878 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01708   0.00331   0.99354   0.66357   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49012 49012 SRR7612977 SRX4477677 SRS3602877 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 111 ZF brain smallRNAseq GSM3309585   source name:brain|strain:AB JxT\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male NH FLI 111 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:brain|age:3.5 years|Sex:male GSM3309585 GSM3309585: NH FLI 111 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309585   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309585 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         743568750.0 14871375.0 GSM3309585 r1 0:50 A:166161134;C:175989827;G:216120925;T:185273082;N:23782 50       166161134 175989827 216120925 185273082 23782 SRX4477677 SRS3602877 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01548   0.00239   0.99515   0.60786   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49013 49013 SRR7612976 SRX4477676 SRS3602906 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 103 104 ZF brain smallRNAseq GSM3309584   source name:brain|strain:AB JxT\xFC|tissue:brain|age:6 month|Sex:male NH FLI 103 104 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:brain|age:6 month|Sex:male GSM3309584 GSM3309584: NH FLI 103 104 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309584   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309584 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         1106423150.0 22128463.0 GSM3309584 r1 0:50 A:234017026;C:276221869;G:334967256;T:261138362;N:78637 50       234017026 276221869 334967256 261138362 78637 SRX4477676 SRS3602906 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.07804   0.00455   0.99263   0.55094   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49014 49014 SRR7612975 SRX4477675 SRS3602876 SRP155545 PRJNA483217 Sequencing of Danio rerio brain for 5 age groups GSE117807 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 101 102 ZF brain smallRNAseq GSM3309583   source name:brain|strain:AB JxT\xFC|tissue:brain|age:6 month|Sex:male NH FLI 101 102 ZF brain smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. brain   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:brain|age:6 month|Sex:male GSM3309583 GSM3309583: NH FLI 101 102 ZF brain smallRNAseq; Danio rerio; ncRNA Seq GSM3309583   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309583 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155545         929857100.0 18597142.0 GSM3309583 r1 0:50 A:195349293;C:237069996;G:279453097;T:217936195;N:48519 50       195349293 237069996 279453097 217936195 48519 SRX4477675 SRS3602876 SRA745937 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01233   0.00233   0.99417   0.76993   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Brain Nervous System
49015 49015 SRR7613129 SRX4477829 SRS3603028 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 100 ZF skin smallRNAseq GSM3309731   source name:skin|strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male NH FLI 100 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male GSM3309731 GSM3309731: NH FLI 100 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309731   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309731 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1018240050.0 20364801.0 GSM3309731 r1 0:50 A:207814229;C:262063346;G:311334117;T:236957867;N:70491 50       207814229 262063346 311334117 236957867 70491 SRX4477829 SRS3603028 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.1074   0.00618   0.9906   0.54934   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49016 49016 SRR7613128 SRX4477828 SRS3603027 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 111 ZF skin smallRNAseq GSM3309730   source name:skin|strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male NH FLI 111 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male GSM3309730 GSM3309730: NH FLI 111 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309730   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309730 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         356381250.0 7127625.0 GSM3309730 r1 0:50 A:70456264;C:88928211;G:109830748;T:87141036;N:24991 50       70456264 88928211 109830748 87141036 24991 SRX4477828 SRS3603027 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.12249   0.00713   0.99299   0.51987   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49017 49017 SRR7613127 SRX4477827 SRS3603046 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 109 ZF skin smallRNAseq GSM3309729   source name:skin|strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male NH FLI 109 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male GSM3309729 GSM3309729: NH FLI 109 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309729   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309729 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         591923400.0 11838468.0 GSM3309729 r1 0:50 A:118873766;C:162031990;G:180619895;T:130356928;N:40821 50       118873766 162031990 180619895 130356928 40821 SRX4477827 SRS3603046 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.09696   0.00911   0.99133   0.52082   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49018 49018 SRR7613126 SRX4477826 SRS3603047 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 108 ZF skin smallRNAseq GSM3309728   source name:skin|strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male NH FLI 108 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male GSM3309728 GSM3309728: NH FLI 108 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309728   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309728 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         736154900.0 14723098.0 GSM3309728 r1 0:50 A:138956520;C:196877364;G:231633259;T:168650452;N:37305 50       138956520 196877364 231633259 168650452 37305 SRX4477826 SRS3603047 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01397   0.0029   0.99312   0.79541   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49019 49019 SRR7613125 SRX4477825 SRS3603026 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 107 ZF skin smallRNAseq GSM3309727   source name:skin|strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male NH FLI 107 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male GSM3309727 GSM3309727: NH FLI 107 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309727   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309727 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         749544400.0 14990888.0 GSM3309727 r1 0:50 A:141473710;C:216076836;G:236230720;T:155730665;N:32469 50       141473710 216076836 236230720 155730665 32469 SRX4477825 SRS3603026 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03825   0.00867   0.99439   0.74015   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49020 49020 SRR7613124 SRX4477824 SRS3603024 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 106 ZF skin smallRNAseq GSM3309726   source name:skin|strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male NH FLI 106 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male GSM3309726 GSM3309726: NH FLI 106 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309726   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309726 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         611281450.0 12225629.0 GSM3309726 r1 0:50 A:111669012;C:149529261;G:189562873;T:160496848;N:23456 50       111669012 149529261 189562873 160496848 23456 SRX4477824 SRS3603024 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02484   0.00442   0.9936   0.64597   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49021 49021 SRR7613123 SRX4477823 SRS3603023 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 150 ZF skin smallRNAseq GSM3309725   source name:skin|strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male NH FLI 150 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male GSM3309725 GSM3309725: NH FLI 150 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309725   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309725 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         2447513950.0 48950279.0 GSM3309725 r1 0:50 A:468043633;C:693473223;G:731577603;T:554251791;N:167700 50       468043633 693473223 731577603 554251791 167700 SRX4477823 SRS3603023 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.07052   0.01139   0.99263   0.59059   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49022 49022 SRR7613122 SRX4477822 SRS3603025 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 149 ZF skin smallRNAseq GSM3309724   source name:skin|strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male NH FLI 149 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male GSM3309724 GSM3309724: NH FLI 149 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309724   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309724 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1871316900.0 37426338.0 GSM3309724 r1 0:50 A:380496272;C:509217150;G:560916561;T:420592548;N:94369 50       380496272 509217150 560916561 420592548 94369 SRX4477822 SRS3603025 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03136   0.00816   0.99488   0.79162   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49023 49023 SRR7613121 SRX4477821 SRS3603022 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 147 ZF skin smallRNAseq GSM3309723   source name:skin|strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male NH FLI 147 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male GSM3309723 GSM3309723: NH FLI 147 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309723   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309723 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         445551200.0 8911024.0 GSM3309723 r1 0:50 A:89205774;C:110497307;G:135908107;T:109919980;N:20032 50       89205774 110497307 135908107 109919980 20032 SRX4477821 SRS3603022 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01905   0.00266   0.99504   0.62127   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49024 49024 SRR7613120 SRX4477820 SRS3603021 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 146 ZF skin smallRNAseq GSM3309722   source name:skin|strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male NH FLI 146 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male GSM3309722 GSM3309722: NH FLI 146 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309722   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309722 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         982200100.0 19644002.0 GSM3309722 r1 0:50 A:192209302;C:247406918;G:306793998;T:235751163;N:38719 50       192209302 247406918 306793998 235751163 38719 SRX4477820 SRS3603021 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02155   0.00424   0.99368   0.62937   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49025 49025 SRR7613119 SRX4477819 SRS3603020 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 145 ZF skin smallRNAseq GSM3309721   source name:skin|strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male NH FLI 145 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male GSM3309721 GSM3309721: NH FLI 145 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309721   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309721 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1336985700.0 26739714.0 GSM3309721 r1 0:50 A:257049527;C:368876598;G:422514962;T:288505412;N:39201 50       257049527 368876598 422514962 288505412 39201 SRX4477819 SRS3603020 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.04358   0.00841   0.99312   0.76026   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49026 49026 SRR7613118 SRX4477818 SRS3603019 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 137 ZF skin smallRNAseq GSM3309720   source name:skin|strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male NH FLI 137 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male GSM3309720 GSM3309720: NH FLI 137 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309720   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309720 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1039359300.0 20787186.0 GSM3309720 r1 0:50 A:200252400;C:286646217;G:322574775;T:229813195;N:72713 50       200252400 286646217 322574775 229813195 72713 SRX4477818 SRS3603019 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.10832   0.00654   0.99113   0.52929   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49027 49027 SRR7613117 SRX4477817 SRS3603018 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 136 ZF skin smallRNAseq GSM3309719   source name:skin|strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male NH FLI 136 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male GSM3309719 GSM3309719: NH FLI 136 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309719   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309719 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         858942900.0 17178858.0 GSM3309719 r1 0:50 A:168340182;C:217323317;G:266544838;T:206688895;N:45668 50       168340182 217323317 266544838 206688895 45668 SRX4477817 SRS3603018 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00791   0.00151   0.99439   0.71291   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49028 49028 SRR7613116 SRX4477816 SRS3603017 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 135 ZF skin smallRNAseq GSM3309718   source name:skin|strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male NH FLI 135 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male GSM3309718 GSM3309718: NH FLI 135 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309718   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309718 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1468015400.0 29360308.0 GSM3309718 r1 0:50 A:275374756;C:419939586;G:454098567;T:318538086;N:64405 50       275374756 419939586 454098567 318538086 64405 SRX4477816 SRS3603017 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01694   0.00341   0.99511   0.72261   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49029 49029 SRR7613115 SRX4477815 SRS3603016 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 134 ZF skin smallRNAseq GSM3309717   source name:skin|strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male NH FLI 134 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male GSM3309717 GSM3309717: NH FLI 134 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309717   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309717 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         678693700.0 13573874.0 GSM3309717 r1 0:50 A:137270784;C:164359833;G:207871154;T:169165189;N:26740 50       137270784 164359833 207871154 169165189 26740 SRX4477815 SRS3603016 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02269   0.00427   0.99295   0.61091   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49030 49030 SRR7613114 SRX4477814 SRS3603015 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 133 ZF skin smallRNAseq GSM3309716   source name:skin|strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male NH FLI 133 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male GSM3309716 GSM3309716: NH FLI 133 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309716   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309716 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         847740400.0 16954808.0 GSM3309716 r1 0:50 A:168475291;C:220114466;G:260254419;T:198870005;N:26219 50       168475291 220114466 260254419 198870005 26219 SRX4477814 SRS3603015 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02431   0.00324   0.99226   0.63318   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49031 49031 SRR7613113 SRX4477813 SRS3603014 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 125 ZF skin smallRNAseq GSM3309715   source name:skin|strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male NH FLI 125 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male GSM3309715 GSM3309715: NH FLI 125 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309715   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309715 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1020735000.0 20414700.0 GSM3309715 r1 0:50 A:205383345;C:253177983;G:308564152;T:253535814;N:73706 50       205383345 253177983 308564152 253535814 73706 SRX4477813 SRS3603014 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.10278   0.00523   0.99155   0.53907   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49032 49032 SRR7613112 SRX4477812 SRS3603012 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 122 ZF skin smallRNAseq GSM3309714   source name:skin|strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male NH FLI 122 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male GSM3309714 GSM3309714: NH FLI 122 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309714   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309714 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         647896400.0 12957928.0 GSM3309714 r1 0:50 A:130330780;C:160929346;G:200383433;T:156218597;N:34244 50       130330780 160929346 200383433 156218597 34244 SRX4477812 SRS3603012 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00732   0.0014   0.99401   0.68357   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49033 49033 SRR7613111 SRX4477811 SRS3603013 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 121 ZF skin smallRNAseq GSM3309713   source name:skin|strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male NH FLI 121 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male GSM3309713 GSM3309713: NH FLI 121 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309713   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309713 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1387064850.0 27741297.0 GSM3309713 r1 0:50 A:262170854;C:395102028;G:446088168;T:283643764;N:60036 50       262170854 395102028 446088168 283643764 60036 SRX4477811 SRS3603013 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01646   0.00363   0.9922   0.73895   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49034 49034 SRR7613110 SRX4477810 SRS3603011 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 120 ZF skin smallRNAseq GSM3309712   source name:skin|strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male NH FLI 120 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male GSM3309712 GSM3309712: NH FLI 120 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309712   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309712 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         771712600.0 15434252.0 GSM3309712 r1 0:50 A:154765175;C:193689306;G:236383702;T:186844174;N:30243 50       154765175 193689306 236383702 186844174 30243 SRX4477810 SRS3603011 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02376   0.00465   0.99166   0.64918   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49035 49035 SRR7613109 SRX4477809 SRS3603010 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 119 ZF skin smallRNAseq GSM3309711   source name:skin|strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male NH FLI 119 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male GSM3309711 GSM3309711: NH FLI 119 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309711   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309711 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         582866200.0 11657324.0 GSM3309711 r1 0:50 A:113005827;C:152497718;G:181963234;T:135381588;N:17833 50       113005827 152497718 181963234 135381588 17833 SRX4477809 SRS3603010 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02894   0.00364   0.99208   0.58438   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49036 49036 SRR7613108 SRX4477808 SRS3603008 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 98 ZF skin smallRNAseq GSM3309710   source name:skin|strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male NH FLI 98 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male GSM3309710 GSM3309710: NH FLI 98 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309710   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309710 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         663294800.0 13265896.0 GSM3309710 r1 0:50 A:137734100;C:161855118;G:201382193;T:162288125;N:35264 50       137734100 161855118 201382193 162288125 35264 SRX4477808 SRS3603008 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00618   0.00111   0.99478   0.65659   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49037 49037 SRR7613107 SRX4477807 SRS3603009 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 96 ZF skin smallRNAseq GSM3309709   source name:skin|strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male NH FLI 96 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male GSM3309709 GSM3309709: NH FLI 96 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309709   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309709 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         569130200.0 11382604.0 GSM3309709 r1 0:50 A:116615049;C:147340637;G:176081367;T:129067210;N:25937 50       116615049 147340637 176081367 129067210 25937 SRX4477807 SRS3603009 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01763   0.00207   0.99389   0.63527   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49038 49038 SRR7613106 SRX4477806 SRS3603007 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 94 ZF skin smallRNAseq GSM3309708   source name:skin|strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male NH FLI 94 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male GSM3309708 GSM3309708: NH FLI 94 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309708   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309708 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         941640450.0 18832809.0 GSM3309708 r1 0:50 A:181731779;C:249059327;G:290464823;T:220348739;N:35782 50       181731779 249059327 290464823 220348739 35782 SRX4477806 SRS3603007 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03203   0.00641   0.98993   0.72488   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49039 49039 SRR7613105 SRX4477805 SRS3603006 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 85 ZF skin smallRNAseq GSM3309707   source name:skin|strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male NH FLI 85 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male GSM3309707 GSM3309707: NH FLI 85 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309707   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309707 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         974950550.0 19499011.0 GSM3309707 r1 0:50 A:188952378;C:263095911;G:305812761;T:217059876;N:29624 50       188952378 263095911 305812761 217059876 29624 SRX4477805 SRS3603006 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03216   0.00571   0.99015   0.67028   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
67037 67037 SRR17007607 SRX13197809 SRS11124869 SRP347244 PRJNA782626 Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content GSE189352 Transcriptome Analysis Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.   pubmed:35628321   VA 6 S6: EVs3 GSM5699732   tissue:EVs3|cell type:extracellular vesicles|strain:kita:RAS VA 6 S6: EVs3 Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample EVs3   RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols. Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid cell type:extracellular vesicles|strain:kita:RAS GSM5699732 GSM5699732: VA 6 S6: EVs3; Danio rerio; ncRNA Seq GSM5699732 r1 GSM5699732 1 RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP347244   loader:fastq load.py VA_6_S6.fastq fastq 1252482921.0 12400821.0 GSM5699732 r1 0:101 A:419008099;C:291188018;G:325856780;T:216362198;N:67826 101       419008099 291188018 325856780 216362198 67826 SRX13197809 SRS11124869 SRA1429699 Experimental Cancer Biology, CIBIO, University of Trento Experimental Cancer Biology, CIBIO, University of Trento 1 0.39065   0.05651   0.9752   0.82248   101   B   usable mapping rate illumina hiseq_era full_length size_fractionation smarter bulk unknown unknown   Italy 2021-11-22 Adult Adult Cancer or Tumor Cancer or Tumor
67038 67038 SRR17007608 SRX13197808 SRS11124868 SRP347244 PRJNA782626 Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content GSE189352 Transcriptome Analysis Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.   pubmed:35628321   VA 5 S5: EVs2 GSM5699731   tissue:EVs2|cell type:extracellular vesicles|strain:kita:RAS VA 5 S5: EVs2 Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample EVs2   RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols. Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid cell type:extracellular vesicles|strain:kita:RAS GSM5699731 GSM5699731: VA 5 S5: EVs2; Danio rerio; ncRNA Seq GSM5699731 r1 GSM5699731 1 RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP347244   loader:fastq load.py VA_5_S5.fastq fastq 1338062039.0 13248139.0 GSM5699731 r1 0:101 A:479478471;C:303639439;G:333339820;T:221533029;N:71280 101       479478471 303639439 333339820 221533029 71280 SRX13197808 SRS11124868 SRA1429699 Experimental Cancer Biology, CIBIO, University of Trento Experimental Cancer Biology, CIBIO, University of Trento 1 0.20158   0.0338   0.98979   0.73724   101   B   usable mapping rate illumina hiseq_era full_length size_fractionation smarter bulk unknown unknown   Italy 2021-11-22 Adult Adult Cancer or Tumor Cancer or Tumor
67039 67039 SRR17007609 SRX13197807 SRS11124867 SRP347244 PRJNA782626 Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content GSE189352 Transcriptome Analysis Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.   pubmed:35628321   VA 4 S4: EVs1 GSM5699730   tissue:EVs1|cell type:extracellular vesicles|strain:kita:RAS VA 4 S4: EVs1 Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample EVs1   RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols. Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid cell type:extracellular vesicles|strain:kita:RAS GSM5699730 GSM5699730: VA 4 S4: EVs1; Danio rerio; ncRNA Seq GSM5699730 r1 GSM5699730 1 RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP347244   loader:fastq load.py VA_4_S4.fastq fastq 1355391215.0 13419715.0 GSM5699730 r1 0:101 A:480538643;C:302531816;G:333018117;T:239227931;N:74708 101       480538643 302531816 333018117 239227931 74708 SRX13197807 SRS11124867 SRA1429699 Experimental Cancer Biology, CIBIO, University of Trento Experimental Cancer Biology, CIBIO, University of Trento 1 0.15363   0.03047   0.98563   0.85818   101   B   usable mapping rate illumina hiseq_era full_length size_fractionation smarter bulk unknown unknown   Italy 2021-11-22 Adult Adult Cancer or Tumor Cancer or Tumor
67040 67040 SRR17007610 SRX13197806 SRS11124866 SRP347244 PRJNA782626 Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content GSE189352 Transcriptome Analysis Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.   pubmed:35628321   VA 24 S14: Melanoma3 GSM5699729   tissue:Melanoma3|cell type:Melanocytes|strain:kita:RAS VA 24 S14: Melanoma3 Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample Melanoma3   RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols. Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid cell type:Melanocytes|strain:kita:RAS GSM5699729 GSM5699729: VA 24 S14: Melanoma3; Danio rerio; ncRNA Seq GSM5699729 r1 GSM5699729 1 RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP347244   loader:fastq load.py VA_24_S14.fastq fastq 1029043954.0 10188554.0 GSM5699729 r1 0:101 A:385266918;C:235984418;G:223100119;T:184638731;N:53768 101       385266918 235984418 223100119 184638731 53768 SRX13197806 SRS11124866 SRA1429699 Experimental Cancer Biology, CIBIO, University of Trento Experimental Cancer Biology, CIBIO, University of Trento 1 0.31444   0.04431   0.97477   0.79077   101   B   usable mapping rate illumina hiseq_era full_length size_fractionation smarter bulk unknown unknown   Italy 2021-11-22 Adult Adult Cancer or Tumor Cancer or Tumor
67041 67041 SRR17007611 SRX13197805 SRS11124865 SRP347244 PRJNA782626 Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content GSE189352 Transcriptome Analysis Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.   pubmed:35628321   VA 23 S13: Melanoma2 GSM5699728   tissue:Melanoma2|cell type:Melanocytes|strain:kita:RAS VA 23 S13: Melanoma2 Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample Melanoma2   RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols. Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid cell type:Melanocytes|strain:kita:RAS GSM5699728 GSM5699728: VA 23 S13: Melanoma2; Danio rerio; ncRNA Seq GSM5699728 r1 GSM5699728 1 RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP347244   loader:fastq load.py VA_23_S13.fastq fastq 1191776669.0 11799769.0 GSM5699728 r1 0:101 A:445740725;C:275311735;G:268819689;T:201841457;N:63063 101       445740725 275311735 268819689 201841457 63063 SRX13197805 SRS11124865 SRA1429699 Experimental Cancer Biology, CIBIO, University of Trento Experimental Cancer Biology, CIBIO, University of Trento 1 0.3168   0.04419   0.96978   0.837   101   B   usable mapping rate illumina hiseq_era full_length size_fractionation smarter bulk unknown unknown   Italy 2021-11-22 Adult Adult Cancer or Tumor Cancer or Tumor
67042 67042 SRR17007612 SRX13197804 SRS11124864 SRP347244 PRJNA782626 Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content GSE189352 Transcriptome Analysis Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.   pubmed:35628321   VA 22 S12: Melanoma1 GSM5699727   tissue:Melanoma1|cell type:Melanocytes|strain:Kita:RAS VA 22 S12: Melanoma1 Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample Melanoma1   RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols. Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid cell type:Melanocytes|strain:Kita:RAS GSM5699727 GSM5699727: VA 22 S12: Melanoma1; Danio rerio; ncRNA Seq GSM5699727 r1 GSM5699727 1 RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.   ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP347244   loader:fastq load.py VA_22_S12.fastq fastq 849183861.0 8407761.0 GSM5699727 r1 0:101 A:315648935;C:198401378;G:181384813;T:153698818;N:49917 101       315648935 198401378 181384813 153698818 49917 SRX13197804 SRS11124864 SRA1429699 Experimental Cancer Biology, CIBIO, University of Trento Experimental Cancer Biology, CIBIO, University of Trento 1 0.37018   0.04901   0.96209   0.55085   101   B   usable mapping rate illumina hiseq_era full_length size_fractionation smarter bulk unknown unknown   Italy 2021-11-22 Adult Adult Cancer or Tumor Cancer or Tumor

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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