RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

6 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "PolyA" and tissue_curation = "Trunk"

✎ View and edit SQL

This data as json, CSV (advanced)

tissue_curation_coarse 1

tissue_curation 1

  • Trunk · 6 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • PolyA · 6 ✖

experiment.library_layout 1

  • SINGLE · 6 ✖

devstage_curation_coarse 1

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
125 125 DRR189379 DRX179844 DRS200410 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 3 SAMD00182222   sample name:Emx3 Larva body 3|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182222 DRX179844 Emx3 / Larva body 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182222       1759409208.0 48872478.0 DRR189379 0:36 A:401147348;C:424523813;G:426350919;T:507310828;N:76300 36       401147348 424523813 426350919 507310828 76300 DRX179844 DRS200410 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.90975   0.11439   0.66076   0.47775   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
126 126 DRR189378 DRX179843 DRS200409 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 2 SAMD00182221   sample name:Emx3 Larva body 2|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182221 DRX179843 Emx3 / Larva body 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182221       1318201020.0 36616695.0 DRR189378 0:36 A:297850068;C:316786585;G:323717530;T:379789606;N:57231 36       297850068 316786585 323717530 379789606 57231 DRX179843 DRS200409 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.9116   0.11269   0.65837   0.46733   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
127 127 DRR189377 DRX179842 DRS200408 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of EMX3 / larval zebrafish 5dpf 1 SAMD00182220   sample name:Emx3 Larva body 1|genotype:Emx3 / |tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182220 DRX179842 Emx3 / Larva body 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182220       812483964.0 22568999.0 DRR189377 0:36 A:185173338;C:197790160;G:197482964;T:232000884;N:36618 36       185173338 197790160 197482964 232000884 36618 DRX179842 DRS200408 DRA008857 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.91107   0.1171   0.65981   0.47458   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
128 128 DRR189376 DRX179841 DRS200449 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 3 SAMD00182219   sample name:WT Larva body 3|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182219 DRX179841 WT Larva body 3 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182219       4030038144.0 111945504.0 DRR189376 0:36 A:943709984;C:971756680;G:977594500;T:1136798448;N:178532 36       943709984 971756680 977594500 1136798448 178532 DRX179841 DRS200449 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.89574   0.12331   0.65831   0.48096   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
129 129 DRR189375 DRX179840 DRS200448 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 2 SAMD00182218   sample name:WT Larva body 2|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182218 DRX179840 WT Larva body 2 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182218       1991670804.0 55324189.0 DRR189375 0:36 A:454367176;C:479012055;G:488407231;T:569793674;N:90668 36       454367176 479012055 488407231 569793674 90668 DRX179840 DRS200448 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.90911   0.12455   0.65494   0.47971   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure
130 130 DRR189374 DRX179839 DRS200447 DRP003977 PRJDB4470 Gene expression analysis of the zebrafish brain DRP003977 Other Gene expression profiling by RNA seq of specific regions and subpopulations of neurons in the zebrafish brain that control behaviors.       Whole body of wild type larval zebrafish 5dpf 1 SAMD00182217   sample name:WT Larva body 1|genotype:wild type|tissue:whole body                 Illumina HiSeq 3000 sequencing of SAMD00182217 DRX179839 WT Larva body 1 1 SureSelect Strand Specific RNA Library Prep Kit   RNA-Seq TRANSCRIPTOMIC PolyA SINGLE ILLUMINA Illumina HiSeq 3000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP003977 Illumina HiSeq 3000 sequencing of SAMD00182217       1018340100.0 28287225.0 DRR189374 0:36 A:233370050;C:244140659;G:247795084;T:292989542;N:44765 36       233370050 244140659 247795084 292989542 44765 DRX179839 DRS200447 DRA008856 NIG|National Institute of Genetics (Japan) National Institute of Genetics (Japan) 1 0.91078   0.12578   0.6524   0.48016   36   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Japan 2021-08-08 Larval Larval Trunk Surface Structure

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");;