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run_metadata

6 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "unspecified" and tissue_curation = "Brain"

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tissue_curation_coarse 1

tissue_curation 1

  • Brain · 6 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • unspecified · 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
37924 37924 SRR1554486 SRX685392 SRS686641 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain2 ZF2Brain2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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> SRP039502     ZF2_Brain_3.fq.gz fastq 1211892536.0 11998936.0 Brain2 Run3 0:101 A:374228993;C:286134640;G:253944548;T:297038575;N:545780 101       374228993 286134640 253944548 297038575 545780 SRX685392 SRS686641 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37928 37928 SRR1554474 SRX685388 SRS566490 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain1 ZFBrain1 2 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</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> SRP039502     ZF1_Brain_3.fq.gz fastq 1192445794.0 11806394.0 Brain1 Run3 0:101 A:369786121;C:268557682;G:265557417;T:288006805;N:537769 101       369786121 268557682 265557417 288006805 537769 SRX685388 SRS566490 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 2e-05   1e-05   1.0       101   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37935 37935 SRR1554484 SRX683268 SRS686641 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain2 ZF2Brain1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF2_Brain_1.fq.gz fastq 654412671.0 12831621.0 Brain2 Run1 0:51 A:160544180;C:166355290;G:168608762;T:158684308;N:220131 51       160544180 166355290 168608762 158684308 220131 SRX683268 SRS686641 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 3e-05   0.0   0.99993   1.0   51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37936 37936 SRR1554485 SRX683268 SRS686641 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF2Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97407|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain2 ZF2Brain1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF2_Brain_2.fq.gz fastq 856322793.0 16790643.0 Brain2 Run2 0:51 A:210706815;C:226772546;G:212404752;T:201722093;N:4716587 51       210706815 226772546 212404752 201722093 4716587 SRX683268 SRS686641 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37943 37943 SRR1554472 SRX481992 SRS566490 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain1 ZFBrain1 1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF1_Brain_1.fq.gz fastq 679860294.0 13330594.0 Brain1 Run1 0:51 A:167202435;C:176450132;G:174468721;T:161497185;N:241821 51       167202435 176450132 174468721 161497185 241821 SRX481992 SRS566490 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System
37944 37944 SRR1554473 SRX481992 SRS566490 SRP039502 PRJNA240316 Danio rerio strain:AB Transcriptome or Gene expression PRJNA240316 Transcriptome Analysis Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.   pubmed:24835514     ZF1Brain1   strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR 97403|sex:male|tissue:Brain|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal                 Zebrafish Brain1 ZFBrain1 1 1 Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit which uses a 3’ adenylated adapter that ligates onto miRs and other small RNAs with a 3’ hydroxyl group.     miRNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</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> SRP039502     ZF1_Brain_2.fq.gz fastq 838372782.0 16438682.0 Brain1 Run2 0:51 A:206906228;C:221202670;G:210716690;T:195319694;N:4227500 51       206906228 221202670 210716690 195319694 4227500 SRX481992 SRS566490 SRA142461 University of Oregon|JHP-Lab University of Oregon 1 0.0   0.0   1.0       51   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna unknown bulk unknown unknown   United States 2014-08-22 Adult Adult Brain Nervous System

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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");;