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run_metadata

4 rows where devstage_curation = "Gastrula" and tissue_curation = "Head"

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tissue_curation_coarse 1

tissue_curation 1

  • Head · 4 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Gastrula · 4 ✖
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
56772 56772 SRR15813417 SRX12105521 SRS10085817 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   flh mut 2 GSM5567791   tissue:flh mutant|strain:floating head mutant n1/n1|Stage:10 hpf|experiment:Mutant embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf. flh mut 2 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz flh mutant   10x Genomcis Chromium single cell preparation   strain:floating head mutant n1/n1|Stage:10 hpf|experiment:Mutant embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf. GSM5567791 GSM5567791: flh mut 2; Danio rerio; RNA Seq GSM5567791   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567791 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate flh_mut_2_possorted_genome_bam.bam 10X Genomics bam file 16092806220.0 178808958.0 GSM5567791 r1 0:90 A:4808364717;C:3262784563;G:3632229222;T:4384293862;N:5133856 90       4808364717 3262784563 3632229222 4384293862 5133856 SRX12105521 SRS10085817 SRA1042742 GEO Washington University in St Louis 1 0.91587   0.25603   0.8199   0.54642   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Head Nervous System
56773 56773 SRR15813416 SRX12105520 SRS10085816 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   flh mut 1 GSM5567790   tissue:flh mutant|strain:floating head mutant n1/n1|Stage:10 hpf|experiment:Mutant embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf. flh mut 1 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz flh mutant   10x Genomcis Chromium single cell preparation   strain:floating head mutant n1/n1|Stage:10 hpf|experiment:Mutant embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf. GSM5567790 GSM5567790: flh mut 1; Danio rerio; RNA Seq GSM5567790   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567790 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate flh_mut_1_possorted_genome_bam.bam 10X Genomics bam file 20399851800.0 226665020.0 GSM5567790 r1 0:90 A:6026150068;C:4212547690;G:4691267625;T:5463467796;N:6418621 90       6026150068 4212547690 4691267625 5463467796 6418621 SRX12105520 SRS10085816 SRA1042742 GEO Washington University in St Louis 1 0.91268   0.26785   0.81288   0.49462   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Head Nervous System
56774 56774 SRR15813415 SRX12105519 SRS10085813 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   flh control 2 GSM5567789   tissue:control of flh mutant|strain:floating head mutant +/+ and +/n1|Stage:10 hpf|experiment:Control embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf. flh control 2 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz control of flh mutant   10x Genomcis Chromium single cell preparation   strain:floating head mutant +/+ and +/n1|Stage:10 hpf|experiment:Control embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf. GSM5567789 GSM5567789: flh control 2; Danio rerio; RNA Seq GSM5567789   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567789 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate flh_control_2_possorted_genome_bam.bam 10X Genomics bam file 24602487300.0 273360970.0 GSM5567789 r1 0:90 A:7284609077;C:5102535766;G:5760617216;T:6447307892;N:7417349 90       7284609077 5102535766 5760617216 6447307892 7417349 SRX12105519 SRS10085813 SRA1042742 GEO Washington University in St Louis 1 0.91331   0.19905   0.82925   0.53189   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Head Nervous System
56775 56775 SRR15813414 SRX12105518 SRS10085811 SRP249509 PRJNA606682 CellOracle: Dissecting cell identity via network inference and in silico gene perturbation GSE145298 Other Single cell RNA sequencing analysis of zebrafish embryos with wild type and crispant sample. Overall design: Single cell RNA sequencing was performed on wild type zebrafish embryos or F0 perturbed embryos using CRISPR Cas9 injection method.   pubmed:36755098   flh control 1 GSM5567788   tissue:control of flh mutant|strain:floating head mutant +/+ and +/n1|Stage:10 hpf|experiment:Control embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf. flh control 1 Generation of fastq files via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Alignment to GRCz11 genome build via https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest Genome build: GRCz11 Supplementary files format and content: barcodes.tsv.gz feature.tsv.gz matrix.mtx.gz control of flh mutant   10x Genomcis Chromium single cell preparation   strain:floating head mutant +/+ and +/n1|Stage:10 hpf|experiment:Control embryos were generated by crossing heterozygous and selecting mutants based on their morphology at 10 hpf. GSM5567788 GSM5567788: flh control 1; Danio rerio; RNA Seq GSM5567788   1 10x Genomcis Chromium single cell preparation GEO Accession:GSM5567788 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 550   SRP249509   assembly:GRCz11|intentional duplicate flh_control_1_possorted_genome_bam.bam 10X Genomics bam file 15510481200.0 172338680.0 GSM5567788 r1 0:90 A:4537923297;C:3229068006;G:3600057890;T:4138746065;N:4685942 90       4537923297 3229068006 3600057890 4138746065 4685942 SRX12105518 SRS10085811 SRA1042742 GEO Washington University in St Louis 1 0.92203   0.24638   0.81274   0.51857   90   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   United States 2021-09-08 Gastrula Embryo Head 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");;