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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"]], "truncated": false, "filtered_table_rows_count": 20, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", 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prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"experiment.platform\" = :p1 order by rowid limit 101", "params": {"p0": "Gastrula", "p1": "ION_TORRENT"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Gastrula&experiment.platform=ION_TORRENT", "results": [{"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 18, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Gastrula&experiment.platform=ION_TORRENT&experiment.library_strategy=miRNA-Seq", "selected": false}, {"value": "RNA-Seq", "label": "RNA-Seq", "count": 2, "toggle_url": 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