{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Gastrula\" and experiment.library_strategy = \"miRNA-Seq\"", "rows": [[39760, "SRR2127901", "SRX1118699", "SRS1011434", "SRP061587", "PRJNA290964", "Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6 hpf 48 hpf zebrafish embryos", "GSE71346", "Transcriptome Analysis", "To investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos. Overall design: Ochratoxin A  mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf ttwo xxx hpf with doses of 0 and 0.5 micromolar.", null, "pubmed:30090366", null, "6 48 0.5\u00b5M OTA [miRNA seq]", "GSM1832841", null, "tissue:embryo control|strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:0.5 \u00b5M ochratoxin A from 6 hpf to 48 hpf", "6 48 0.5\u00b5M OTA [miRNA seq]", "Initially  the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads post filtering low quality data were analyzed using miRDeep2 to clip the 3\u2032 adapter sequence and discarding reads shorter than 18 nucleotides  before aligning reads to the  Zebrafish  genome from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection  since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs  and also identifies novel miRNAs. Genome build: GCF 000002035.4 Supplementary files format and content: bed file for the location of miRNA mapped to chromosome", "embryo control", "6 hpf embryos  were treated with ochratoxin A 0.5 mM till 48 hpf.", "Total RNA was extracted by Trizol\u00ae Reagent Invitrogen  USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology  USA and qualitated by using a Bioanalyzer 2100 Agilent Technology  USA with RNA 6000 labchip kit Agilent Technologies  USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene  Taipei  Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3\u2032 and 5\u2032 adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters.\u00a0 Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software", "zebrafish embryos were selected at 6 hph with normal development.", "strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:0.5 \u00b5M ochratoxin A from 6 hpf to 48 hpf", "GSM1832841", "GSM1832841: 6 48 0.5\u00b5M OTA [miRNA seq]; Danio rerio; miRNA Seq", "GSM1832841", null, "1", "Total RNA was extracted by Trizol\u00ae Reagent Invitrogen  USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology  USA and qualitated by using a Bioanalyzer 2100 Agilent Technology  USA with RNA 6000 labchip kit Agilent Technologies  USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene  Taipei  Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3\u2032 and 5\u2032 adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters.\u00a0 Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . 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Overall design: Ochratoxin A  mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf ttwo xxx hpf with doses of 0 and 0.5 micromolar.", null, "pubmed:30090366", null, "6 48 control [miRNA seq]", "GSM1832840", null, "tissue:embryo control|strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:n1 control", "6 48 control [miRNA seq]", "Initially  the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads post filtering low quality data were analyzed using miRDeep2 to clip the 3\u2032 adapter sequence and discarding reads shorter than 18 nucleotides  before aligning reads to the  Zebrafish  genome from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection  since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs  and also identifies novel miRNAs. Genome build: GCF 000002035.4 Supplementary files format and content: bed file for the location of miRNA mapped to chromosome", "embryo control", "6 hpf embryos  were treated with ochratoxin A 0.5 mM till 48 hpf.", "Total RNA was extracted by Trizol\u00ae Reagent Invitrogen  USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology  USA and qualitated by using a Bioanalyzer 2100 Agilent Technology  USA with RNA 6000 labchip kit Agilent Technologies  USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene  Taipei  Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3\u2032 and 5\u2032 adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters.\u00a0 Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software", "zebrafish embryos were selected at 6 hph with normal development.", "strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:n1 control", "GSM1832840", "GSM1832840: 6 48 control [miRNA seq]; Danio rerio; miRNA Seq", "GSM1832840", null, "1", "Total RNA was extracted by Trizol\u00ae Reagent Invitrogen  USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology  USA and qualitated by using a Bioanalyzer 2100 Agilent Technology  USA with RNA 6000 labchip kit Agilent Technologies  USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene  Taipei  Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3\u2032 and 5\u2032 adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters.\u00a0 Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . 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Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_006_rawlib.basecaller.bam", "bam", 41157611.0, 1592351.0, "IonXpressRNA 006 rawlib.basecaller.bam", "0:25.85", "A:11322629;C:9228187;G:9750979;T:10855816;N:0", 25, null, null, null, 11322629, 9228187, 9750979, 10855816, 0, "SRX2267729", "SRS1758934", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.63095, null, 0.40683, null, 0.8003, null, 0.56985, null, 29, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41463, "SRR4449272", "SRX2267728", "SRS1758932", "SRP092030", "PRJNA350377", "Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly", "PRJNA350377", "Transcriptome Analysis", "Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly", null, null, "Danio rerio embryo at approx. 50% epiboly", "Danio rerio embryo at approx. 50% epiboly", "S03 RID0445", null, "strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "S03", "S03 RID0445", "S03 RID0445", "Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_003_rawlib.basecaller.bam", "bam", 60356442.0, 2057592.0, "IonXpressRNA 003 rawlib.basecaller.bam", "0:29.33", "A:17060096;C:13661341;G:13721228;T:15913777;N:0", 29, null, null, null, 17060096, 13661341, 13721228, 15913777, 0, "SRX2267728", "SRS1758932", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.73029, null, 0.49935, null, 0.8225, null, 0.56029, null, 30, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41464, "SRR4449271", "SRX2267727", "SRS1758931", "SRP092030", "PRJNA350377", "Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly", "PRJNA350377", "Transcriptome Analysis", "Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly", null, null, "Danio rerio embryo at approx. 50% epiboly", "Danio rerio embryo at approx. 50% epiboly", "S04 RID0445", null, "strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "S04", "S04 RID0445", "S04 RID0445", "Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_004_rawlib.basecaller.bam", "bam", 55705225.0, 2055064.0, "IonXpressRNA 004 rawlib.basecaller.bam", "0:27.11", "A:15806355;C:12308008;G:12579212;T:15011650;N:0", 27, null, null, null, 15806355, 12308008, 12579212, 15011650, 0, "SRX2267727", "SRS1758931", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.70796, null, 0.49815, null, 0.81444, null, 0.54452, null, 41, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41465, "SRR4449270", "SRX2267726", "SRS1758930", "SRP092030", "PRJNA350377", "Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly", "PRJNA350377", "Transcriptome Analysis", "Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly", null, null, "Danio rerio embryo at approx. 50% epiboly", "Danio rerio embryo at approx. 50% epiboly", "S01 RID0445", null, "strain:ABTL|dev stage:50% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "S01", "S01 RID0445", "S01 RID0445", "Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_001_rawlib.basecaller.bam", "bam", 35407241.0, 1342552.0, "IonXpressRNA 001 rawlib.basecaller.bam", "0:26.37", "A:9988109;C:7841340;G:8187069;T:9390723;N:0", 26, null, null, null, 9988109, 7841340, 8187069, 9390723, 0, "SRX2267726", "SRS1758930", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.63621, null, 0.43661, null, 0.80992, null, 0.53899, null, 31, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41466, "SRR4449269", "SRX2267725", "SRS1758928", "SRP092030", "PRJNA350377", "Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly", "PRJNA350377", "Transcriptome Analysis", "Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly", null, null, "Danio rerio embryo at approx. 50% epiboly", "Danio rerio embryo at approx. 50% epiboly", "S02 RID0445", null, "strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "S02", "S02 RID0445", "S02 RID0445", "Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_002_rawlib.basecaller.bam", "bam", 40875445.0, 1512601.0, "IonXpressRNA 002 rawlib.basecaller.bam", "0:27.02", "A:11593378;C:9124451;G:9444184;T:10713432;N:0", 27, null, null, null, 11593378, 9124451, 9444184, 10713432, 0, "SRX2267725", "SRS1758928", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.66621, null, 0.45417, null, 0.8127, null, 0.55033, null, 21, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41467, "SRR4449267", "SRX2267724", "SRS1758927", "SRP092030", "PRJNA350377", "Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly", "PRJNA350377", "Transcriptome Analysis", "Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly", null, null, "Danio rerio embryo at approx. 50% epiboly", "Danio rerio embryo at approx. 50% epiboly", "S15 RID0445", null, "strain:ABTL|dev stage:52% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "S15", "S15 RID0445", "S15 RID0445", "Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_015_rawlib.basecaller.bam", "bam", 58421266.0, 2091074.0, "IonXpressRNA 015 rawlib.basecaller.bam", "0:27.94", "A:16715618;C:13019609;G:13014639;T:15671400;N:0", 27, null, null, null, 16715618, 13019609, 13014639, 15671400, 0, "SRX2267724", "SRS1758927", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.71786, null, 0.51457, null, 0.83863, null, 0.53442, null, 29, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41468, "SRR4449266", "SRX2267723", "SRS1758929", "SRP092030", "PRJNA350377", "Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly", "PRJNA350377", "Transcriptome Analysis", "Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly", null, null, "Danio rerio embryo at approx. 50% epiboly", "Danio rerio embryo at approx. 50% epiboly", "S16 RID0445", null, "strain:ABTL|dev stage:54% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "S16", "S16 RID0445", "S16 RID0445", "Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_016_rawlib.basecaller.bam", "bam", 55022551.0, 2073507.0, "IonXpressRNA 016 rawlib.basecaller.bam", "0:26.54", "A:15319738;C:12288588;G:12653066;T:14761159;N:0", 26, null, null, null, 15319738, 12288588, 12653066, 14761159, 0, "SRX2267723", "SRS1758929", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.68905, null, 0.46941, null, 0.80306, null, 0.55981, null, 26, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41469, "SRR4449265", "SRX2267722", "SRS1758926", "SRP092030", "PRJNA350377", "Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly", "PRJNA350377", "Transcriptome Analysis", "Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly", null, null, "Danio rerio embryo at approx. 50% epiboly", "Danio rerio embryo at approx. 50% epiboly", "S13 RID0445", null, "strain:ABTL|dev stage:55% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "S13", "S13 RID0445", "S13 RID0445", "Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_013_rawlib.basecaller.bam", "bam", 49641484.0, 2028008.0, "IonXpressRNA 013 rawlib.basecaller.bam", "0:24.48", "A:13840820;C:11016762;G:11715475;T:13068427;N:0", 24, null, null, null, 13840820, 11016762, 11715475, 13068427, 0, "SRX2267722", "SRS1758926", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.55355, null, 0.3659, null, 0.81576, null, 0.55987, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41470, "SRR4449264", "SRX2267721", "SRS1758925", "SRP092030", "PRJNA350377", "Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly", "PRJNA350377", "Transcriptome Analysis", "Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly", null, null, "Danio rerio embryo at approx. 50% epiboly", "Danio rerio embryo at approx. 50% epiboly", "S14 RID0445", null, "strain:ABTL|dev stage:56% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "S14", "S14 RID0445", "S14 RID0445", "Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_014_rawlib.basecaller.bam", "bam", 52969826.0, 2019609.0, "IonXpressRNA 014 rawlib.basecaller.bam", "0:26.23", "A:14762618;C:11847782;G:12164393;T:14195033;N:0", 26, null, null, null, 14762618, 11847782, 12164393, 14195033, 0, "SRX2267721", "SRS1758925", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.65926, null, 0.45113, null, 0.80515, null, 0.56221, null, 22, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41471, "SRR4449263", "SRX2267720", "SRS1758923", "SRP092030", "PRJNA350377", "Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly", "PRJNA350377", "Transcriptome Analysis", "Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly", null, null, "Danio rerio embryo at approx. 50% epiboly", "Danio rerio embryo at approx. 50% epiboly", "S11 RID0445", null, "strain:ABTL|dev stage:56% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "S11", "S11 RID0445", "S11 RID0445", "Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_011_rawlib.basecaller.bam", "bam", 54877334.0, 2122171.0, "IonXpressRNA 011 rawlib.basecaller.bam", "0:25.86", "A:14884144;C:12539815;G:13173981;T:14279394;N:0", 25, null, null, null, 14884144, 12539815, 13173981, 14279394, 0, "SRX2267720", "SRS1758923", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.62581, null, 0.40704, null, 0.82002, null, 0.59605, null, 20, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41472, "SRR4449262", "SRX2267719", "SRS1758924", "SRP092030", "PRJNA350377", "Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly", "PRJNA350377", "Transcriptome Analysis", "Small RNAseq experiment of individual embryos from the 8 different spawns  taken at gastrulation at approximately 50% epiboly", null, null, "Danio rerio embryo at approx. 50% epiboly", "Danio rerio embryo at approx. 50% epiboly", "S12 RID0445", null, "strain:ABTL|dev stage:53% epiboly|sex:not applicable|tissue:whole embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "S12", "S12 RID0445", "S12 RID0445", "Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP092030", null, null, "IonXpressRNA_012_rawlib.basecaller.bam", "bam", 51987914.0, 1937451.0, "IonXpressRNA 012 rawlib.basecaller.bam", "0:26.83", "A:14499922;C:11778716;G:11957347;T:13751929;N:0", 26, null, null, null, 14499922, 11778716, 11957347, 13751929, 0, "SRX2267719", "SRS1758924", "SRA486759", "UNIVERSITY OF AMSTERDAM, SILS|RB&AB", "UNIVERSITY OF AMSTERDAM, SILS", 1, 0.67286, null, 0.44698, null, 0.80919, null, 0.58291, null, 29, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2017-11-01", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59623, "SRR11974583", "SRX8518005", "SRS6815486", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Gamma2 nmbu sncRNA 3", "GSM4605882", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "F1 Gamma2 nmbu sncRNA 3", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "GSM4605882", "GSM4605882: F1 Gamma2 nmbu sncRNA 3; Danio rerio; miRNA Seq", "GSM4605882", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605882", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_6_raw.fq.gz", "fastq", 566507200.0, 11330144.0, "GSM4605882 r1", "0:50", "A:167677443;C:125843251;G:148647392;T:124217714;N:121400", 50, null, null, null, 167677443, 125843251, 148647392, 124217714, 121400, "SRX8518005", "SRS6815486", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.75254, null, 0.48205, null, 0.84346, null, 0.59219, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59624, "SRR11974582", "SRX8518004", "SRS6815485", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Gamma2 nmbu sncRNA 2", "GSM4605881", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "F1 Gamma2 nmbu sncRNA 2", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "GSM4605881", "GSM4605881: F1 Gamma2 nmbu sncRNA 2; Danio rerio; miRNA Seq", "GSM4605881", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605881", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_5_raw.fq.gz", "fastq", 579779650.0, 11595593.0, "GSM4605881 r1", "0:50", "A:173232869;C:126599907;G:152751070;T:127092652;N:103152", 50, null, null, null, 173232869, 126599907, 152751070, 127092652, 103152, "SRX8518004", "SRS6815485", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.7644, null, 0.48211, null, 0.84583, null, 0.59288, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59625, "SRR11974581", "SRX8518003", "SRS6815484", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Gamma1 nmbu sncRNA 1", "GSM4605880", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "F1 Gamma1 nmbu sncRNA 1", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "GSM4605880", "GSM4605880: F1 Gamma1 nmbu sncRNA 1; Danio rerio; miRNA Seq", "GSM4605880", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605880", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_4_raw.fq.gz", "fastq", 649357050.0, 12987141.0, "GSM4605880 r1", "0:50", "A:191891965;C:145644319;G:171130267;T:140550711;N:139788", 50, null, null, null, 191891965, 145644319, 171130267, 140550711, 139788, "SRX8518003", "SRS6815484", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.75002, null, 0.44712, null, 0.84818, null, 0.57467, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59626, "SRR11974580", "SRX8518002", "SRS6815483", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Control3 nmbu sncRNA 3", "GSM4605879", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "F1 Control3 nmbu sncRNA 3", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "GSM4605879", "GSM4605879: F1 Control3 nmbu sncRNA 3; Danio rerio; miRNA Seq", "GSM4605879", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605879", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_3_raw.fq.gz", "fastq", 641762600.0, 12835252.0, "GSM4605879 r1", "0:50", "A:187476040;C:147628502;G:173061052;T:133488938;N:108068", 50, null, null, null, 187476040, 147628502, 173061052, 133488938, 108068, "SRX8518002", "SRS6815483", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.68333, null, 0.36693, null, 0.8493, null, 0.57501, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59627, "SRR11974579", "SRX8518001", "SRS6815482", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Control2 nmbu sncRNA 2", "GSM4605878", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "F1 Control2 nmbu sncRNA 2", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "GSM4605878", "GSM4605878: F1 Control2 nmbu sncRNA 2; Danio rerio; miRNA Seq", "GSM4605878", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605878", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_2_raw.fq.gz", "fastq", 531815250.0, 10636305.0, "GSM4605878 r1", "0:50", "A:155930702;C:122952623;G:141743533;T:111074299;N:114093", 50, null, null, null, 155930702, 122952623, 141743533, 111074299, 114093, "SRX8518001", "SRS6815482", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.65896, null, 0.35164, null, 0.8453, null, 0.57438, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59628, "SRR11974578", "SRX8518000", "SRS6815481", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Control1 nmbu sncRNA 1", "GSM4605877", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "F1 Control1 nmbu sncRNA 1", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "GSM4605877", "GSM4605877: F1 Control1 nmbu sncRNA 1; Danio rerio; miRNA Seq", "GSM4605877", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605877", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_1_raw.fq.gz", "fastq", 534855250.0, 10697105.0, "GSM4605877 r1", "0:50", "A:156249541;C:120087413;G:145230236;T:113171967;N:116093", 50, null, null, null, 156249541, 120087413, 145230236, 113171967, 116093, "SRX8518000", "SRS6815481", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.74031, null, 0.40182, null, 0.83366, null, 0.60438, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [60891, "SRR12628230", "SRX9110493", "SRS7353476", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected  miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition  miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf  shield stage  11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs", null, "pubmed:33506864", null, "h6 2: PGCs 6hpf repeat2", "GSM4777190", null, "source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad", "h6 2: PGCs 6hpf repeat2", "Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample \u2026", "PGCs", null, "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", null, "cell type:primordial germ cells|strain:AB|tissue:gonad", "GSM4777190", "GSM4777190: h6 2: PGCs 6hpf repeat2; Danio rerio; miRNA Seq", "GSM4777190", null, "1", "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", "GEO Accession:GSM4777190", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP282187", null, null, "h6_2.fastq", "fastq", 2330922150.0, 15539481.0, "GSM4777190 r1", "0:150 1:0", "A:563758043;C:619336180;G:552040747;T:595747277;N:39903", 150, 0, null, null, 563758043, 619336180, 552040747, 595747277, 39903, "SRX9110493", "SRS7353476", "SRA1124474", "GEO", "Shanghai Institute of Biochemistry and Cell Biology,CAS", 1, 0.00014, null, 0.0, null, 0.99997, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-12", "Gastrula", "Embryo", "Gonad", "Reproductive System"], [60892, "SRR12628229", "SRX9110492", "SRS7353475", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected  miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition  miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf  shield stage  11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs", null, "pubmed:33506864", null, "h6 1: PGCs 6hpf repeat1", "GSM4777189", null, "source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad", "h6 1: PGCs 6hpf repeat1", "Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample \u2026", "PGCs", null, "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", null, "cell type:primordial germ cells|strain:AB|tissue:gonad", "GSM4777189", "GSM4777189: h6 1: PGCs 6hpf repeat1; Danio rerio; miRNA Seq", "GSM4777189", null, "1", "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", "GEO Accession:GSM4777189", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP282187", null, null, "h6_1.fastq", "fastq", 1979588400.0, 13197256.0, "GSM4777189 r1", "0:150 1:0", "A:453046525;C:471873747;G:495904656;T:558729697;N:33775", 150, 0, null, null, 453046525, 471873747, 495904656, 558729697, 33775, "SRX9110492", "SRS7353475", "SRA1124474", "GEO", "Shanghai Institute of Biochemistry and Cell Biology,CAS", 1, 0.00028, null, 0.0, null, 0.99997, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-12", "Gastrula", "Embryo", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 28, "expanded_columns": [], 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