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run_metadata

8 rows where experiment.library_selection = "cDNA", experiment.library_strategy = "miRNA-Seq" and experiment.platform = "ILLUMINA"

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devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

  • ILLUMINA · 8 ✖

experiment.library_strategy 1

  • miRNA-Seq · 8 ✖

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 8 ✖

experiment.library_layout 1

devstage_curation_coarse 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
63794 63794 SRR14066768 SRX10441285 SRS8573413 SRP312051 PRJNA716861 Zebrafish Bdnf CRISPR/CAS9 knock out PRJNA716861 Other RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish         SD 10   strain:AB|isolate:WT24 small2|age:24 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio Bdnf mutant Bdnf Libr10 Bdnf Libr10 Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP312051     WT24_small2_R1_001.fastq.gz fastq 1328140584.0 17475534.0 WT24 small2 R1 001.fastq.gz 0:76 1:0 A:412652031;C:328228938;G:257910677;T:329318258;N:30680 76 0     412652031 328228938 257910677 329318258 30680 SRX10441285 SRS8573413 SRA1209895 Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms Stazione Zoologica Anton Dohrn 1 0.00121   0.00038   0.99918   0.74603   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Italy 2021-03-25 Multi-stage Embryo Whole Organism All anatomical structures
63795 63795 SRR14066769 SRX10441284 SRS8573412 SRP312051 PRJNA716861 Zebrafish Bdnf CRISPR/CAS9 knock out PRJNA716861 Other RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish         SD 9   strain:AB|isolate:WT24 small1|age:24 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio Bdnf mutant Bdnf Libr9 Bdnf Libr9 Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP312051     WT24_small1_R1_001.fastq.gz fastq 1219490832.0 16045932.0 WT24 small1 R1 001.fastq.gz 0:76 1:0 A:351083382;C:291591654;G:283111351;T:293679894;N:24551 76 0     351083382 291591654 283111351 293679894 24551 SRX10441284 SRS8573412 SRA1209895 Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms Stazione Zoologica Anton Dohrn 1 0.00842   0.00219   0.99786   0.61991   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Italy 2021-03-25 Multi-stage Embryo Whole Organism All anatomical structures
63802 63802 SRR14066779 SRX10441277 SRS8573405 SRP312051 PRJNA716861 Zebrafish Bdnf CRISPR/CAS9 knock out PRJNA716861 Other RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish         SD 16   strain:AB|isolate:MUT48 small4|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio Bdnf mutant Bdnf Libr16 Bdnf Libr16 Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP312051     MUT48_small4_R1_001.fastq.gz fastq 1346335212.0 17714937.0 MUT48 small4 R1 001.fastq.gz 0:76 1:0 A:416374120;C:317460666;G:293419951;T:319049435;N:31040 76 0     416374120 317460666 293419951 319049435 31040 SRX10441277 SRS8573405 SRA1209895 Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms Stazione Zoologica Anton Dohrn 1 0.00179   0.00093   0.99935   0.5625   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Italy 2021-03-25 Hatching Embryo Whole Organism All anatomical structures
63803 63803 SRR14066776 SRX10441276 SRS8573404 SRP312051 PRJNA716861 Zebrafish Bdnf CRISPR/CAS9 knock out PRJNA716861 Other RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish         SD 15   strain:AB|isolate:MUT48 small3|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio Bdnf mutant Bdnf Libr15 Bdnf Libr15 Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP312051     MUT48_small3_R1_001.fastq.gz fastq 1304806760.0 17168510.0 MUT48 small3 R1 001.fastq.gz 0:76 1:0 A:387991384;C:335175146;G:279195316;T:302418185;N:26729 76 0     387991384 335175146 279195316 302418185 26729 SRX10441276 SRS8573404 SRA1209895 Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms Stazione Zoologica Anton Dohrn 1 0.00621   0.00334   0.99926   0.64343   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Italy 2021-03-25 Hatching Embryo Whole Organism All anatomical structures
63804 63804 SRR14066777 SRX10441275 SRS8573403 SRP312051 PRJNA716861 Zebrafish Bdnf CRISPR/CAS9 knock out PRJNA716861 Other RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish         SD 14   strain:AB|isolate:WT48 small4|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio Bdnf mutant Bdnf Libr14 Bdnf Libr14 Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP312051     WT48_small4_R1_001.fastq.gz fastq 1339796780.0 17628905.0 WT48 small4 R1 001.fastq.gz 0:76 1:0 A:416769744;C:315222509;G:273799428;T:333973227;N:31872 76 0     416769744 315222509 273799428 333973227 31872 SRX10441275 SRS8573403 SRA1209895 Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms Stazione Zoologica Anton Dohrn 1 0.00503   0.00127   0.99888   0.67632   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Italy 2021-03-25 Hatching Embryo Whole Organism All anatomical structures
63805 63805 SRR14066778 SRX10441274 SRS8573402 SRP312051 PRJNA716861 Zebrafish Bdnf CRISPR/CAS9 knock out PRJNA716861 Other RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish         SD 13   strain:AB|isolate:WT48 small3|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio Bdnf mutant Bdnf Libr13 Bdnf Libr13 Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP312051     WT48_small3_R1_001.fastq.gz fastq 1212286260.0 15951135.0 WT48 small3 R1 001.fastq.gz 0:76 1:0 A:374600889;C:299473187;G:252454435;T:285727773;N:29976 76 0     374600889 299473187 252454435 285727773 29976 SRX10441274 SRS8573402 SRA1209895 Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms Stazione Zoologica Anton Dohrn 1 0.01297   0.00494   0.99849   0.661   76   B   usable mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Italy 2021-03-25 Hatching Embryo Whole Organism All anatomical structures
63806 63806 SRR14066780 SRX10441273 SRS8573401 SRP312051 PRJNA716861 Zebrafish Bdnf CRISPR/CAS9 knock out PRJNA716861 Other RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish         SD 12   strain:AB|isolate:MUT24 small2|age:24 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio Bdnf mutant Bdnf Libr12 Bdnf Libr12 Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP312051     MUT24_small2_R1_001.fastq.gz fastq 1214643400.0 15982150.0 MUT24 small2 R1 001.fastq.gz 0:76 1:0 A:339563536;C:303989834;G:244843758;T:326220311;N:25961 76 0     339563536 303989834 244843758 326220311 25961 SRX10441273 SRS8573401 SRA1209895 Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms Stazione Zoologica Anton Dohrn 1 0.00526   0.00203   0.99876   0.62659   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Italy 2021-03-25 Multi-stage Embryo Whole Organism All anatomical structures
63807 63807 SRR14066781 SRX10441272 SRS8573400 SRP312051 PRJNA716861 Zebrafish Bdnf CRISPR/CAS9 knock out PRJNA716861 Other RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish         SD 11   strain:AB|isolate:MUT24 small1|age:24 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio Bdnf mutant Bdnf Libr11 Bdnf Libr11 Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.     miRNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP312051     MUT24_small1_R1_001.fastq.gz fastq 1273652916.0 16758591.0 MUT24 small1 R1 001.fastq.gz 0:76 1:0 A:398579242;C:309782360;G:268224898;T:297035166;N:31250 76 0     398579242 309782360 268224898 297035166 31250 SRX10441272 SRS8573400 SRA1209895 Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms Stazione Zoologica Anton Dohrn 1 0.00191   0.0006   0.9992   0.60752   76   T   under 1.2% mapping rate illumina hiseq_era unknown small_rna trueseq bulk bulk bulk   Italy 2021-03-25 Multi-stage Embryo Whole Organism All anatomical structures

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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");;