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run_metadata

6 rows where experiment.library_selection = "Oligo-dT", technology = "10x" and tissue_curation_coarse = "Liver and Biliary System"

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devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

  • Liver and Biliary System · 6 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • Oligo-dT · 6 ✖

experiment.library_layout 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
70706 70706 SRR21457012 SRX17460721 SRS15014532 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Liver in the WT S4 L004   isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 4|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf wild type liver Live S4 L004 aliquot 4 Live S4 L004 aliquot 4 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S4_Live_20200825NB_S4_L004_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L004_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L004_R2_001.fastq.gz fastq fastq fastq 15359722785.0 82137555.0 20200806 S4 Live 20200825NB S4 L004 I1 001.fastq.gz 0:8 1:28 2:151 A:3860252969;C:2756020453;G:2781498176;T:3004915512;N:83695 8 28 151   3860252969 2756020453 2781498176 3004915512 83695 SRX17460721 SRS15014532 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.90519   0.06757   0.88243   0.74961   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Liver Liver and Biliary System
70707 70707 SRR21457013 SRX17460720 SRS15014531 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Liver in the WT S4 L003   isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 3|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf wild type liver Live S4 L003 aliquot 3 Live S4 L003 aliquot 3 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S4_Live_20200825NB_S4_L003_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L003_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L003_R2_001.fastq.gz fastq fastq fastq 15277905984.0 81700032.0 20200806 S4 Live 20200825NB S4 L003 I1 001.fastq.gz 0:8 1:28 2:151 A:3834498109;C:2745604041;G:2766967723;T:2989497144;N:137815 8 28 151   3834498109 2745604041 2766967723 2989497144 137815 SRX17460720 SRS15014531 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.90792   0.06795   0.88089   0.75291   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Liver Liver and Biliary System
70710 70710 SRR21457016 SRX17460717 SRS15014528 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Liver in the WT S4 L002   isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 2|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf wild type liver Live S4 L002 aliquot 2 Live S4 L002 aliquot 2 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S4_Live_20200825NB_S4_L002_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L002_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L002_R2_001.fastq.gz fastq fastq fastq 15033903335.0 80395205.0 20200806 S4 Live 20200825NB S4 L002 I1 001.fastq.gz 0:8 1:28 2:151 A:3774023536;C:2701104584;G:2719224706;T:2945204367;N:118762 8 28 151   3774023536 2701104584 2719224706 2945204367 118762 SRX17460717 SRS15014528 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.90993   0.06896   0.88002   0.75003   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Liver Liver and Biliary System
70711 70711 SRR21457017 SRX17460716 SRS15014527 SRP385641 PRJNA857143 Single cell transcriptomic data of zebrafish lbw mutant PRJNA857143 Other Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.         Liver in the WT S4 L001   isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 1|BioSampleModel:Model organism or animal                 scRNA Seq of zebrafish: 6 dpf wild type liver Live S4 L001 aliquot 1 Live S4 L001 aliquot 1 using Chromium Single Cell three prime GEM v3.1 Reagent Kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP385641     20200806_S4_Live_20200825NB_S4_L001_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L001_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L001_R2_001.fastq.gz fastq fastq fastq 15047379303.0 80467269.0 20200806 S4 Live 20200825NB S4 L001 I1 001.fastq.gz 0:8 1:28 2:151 A:3778269770;C:2702450055;G:2724848747;T:2944890394;N:98653 8 28 151   3778269770 2702450055 2724848747 2944890394 98653 SRX17460716 SRS15014527 SRA1491985 Southwest University|Institute of Developmental Biology and Regenerativ Southwest University 1 0.90977   0.06799   0.87998   0.75241   151   B   usable mapping rate illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2022-09-11 Larval Larval Liver Liver and Biliary System
75608 75608 SRR24742192 SRX20519420 SRS17829368 SRP439656 PRJNA975724 Key factors in the process of biliary epithelial cells to bipotential progenitor cells dedifferentiation PRJNA975724 Other Uncover the regulatory mechanisms underlying biliary cell dedifferentiation.     The fish were treated with mtz at 5 dpf and then the livers were collected post 24 hours treatment namly regeneration 0 hour. scRNA seq of zebrafish R0h livers Livers of lfabp:Dendra2 NTR fish at mtz R0h   strain:ABGO|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:mtz R0h|sex:pooled male and female|tissue:liver|birth location:China|collection date:2021 04 29|geo loc name:China: Chongqing|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish R0h livers 20210429 S3 R0 20210429 S3 R0 Using Chromium Single cell three prime GEM v3.1 Reagent kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439656     R21049148-20210429-S3-R0-1_combined_R1.fastq.gz R21049148-20210429-S3-R0-1_combined_R2.fastq.gz R21049148-20210429-S3-R0-2_combined_R1.fastq.gz R21049148-20210429-S3-R0-2_combined_R2.fastq.gz R21049148-20210429-S3-R0-3_combined_R1.fastq.gz R21049148-20210429-S3-R0-3_combined_R2.fastq.gz R21049148-20210429-S3-R0-4_combined_R1.fastq.gz R21049148-20210429-S3-R0-4_combined_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq 108860887800.0 362869626.0 R21049148 20210429 S3 R0 1 combined R1.fastq.gz 0:150 1:150 A:46078842047;C:20145501988;G:19787836142;T:22846772612;N:1935011 150 150     46078842047 20145501988 19787836142 22846772612 1935011 SRX20519420 SRS17829368 SRA1643264 Institute of Developmental Biology and Regenerative Medicine|Southwest University Institute of Developmental Biology and Regenerative Medicine AccuraMed Company 2 0.0 0.92113 0.0 0.15798 1.0 0.81215   0.58532 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2023-05-25 Zygote Embryo Liver Liver and Biliary System
75609 75609 SRR24742193 SRX20519419 SRS17829369 SRP439656 PRJNA975724 Key factors in the process of biliary epithelial cells to bipotential progenitor cells dedifferentiation PRJNA975724 Other Uncover the regulatory mechanisms underlying biliary cell dedifferentiation.     The livers of fish were collected at 6 dpf scRNA seq of zebrafish 6 dpf livers Livers of lfabp:Dendra2 NTR fish at 6 dpf   strain:ABGO|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:6 dpf|sex:pooled male and female|tissue:liver|birth location:China|collection date:2021 04 29|geo loc name:China: Chongqing|BioSampleModel:Model organism or animal                 scRNA seq of zebrafish 6 dpf livers 20210429 S2 D6 20210429 S2 D6 Using Chromium Single cell three prime GEM v3.1 Reagent kit     RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP439656     R21049147-20210429-S2-D6-1_combined_R1.fastq.gz R21049147-20210429-S2-D6-1_combined_R2.fastq.gz R21049147-20210429-S2-D6-2_combined_R1.fastq.gz R21049147-20210429-S2-D6-2_combined_R2.fastq.gz R21049147-20210429-S2-D6-3_combined_R1.fastq.gz R21049147-20210429-S2-D6-3_combined_R2.fastq.gz R21049147-20210429-S2-D6-4_combined_R1.fastq.gz R21049147-20210429-S2-D6-4_combined_R2.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq 122319275400.0 407730918.0 R21049147 20210429 S2 D6 1 combined R1.fastq.gz 0:150 1:150 A:36198844657;C:27630980168;G:25561495158;T:32927451902;N:503515 150 150     36198844657 27630980168 25561495158 32927451902 503515 SRX20519419 SRS17829369 SRA1643264 Institute of Developmental Biology and Regenerative Medicine|Southwest University Institute of Developmental Biology and Regenerative Medicine AccuraMed Company 2 0.00072 0.9132 0.00023 0.11357 0.99995 0.88909 0.5 0.69408 150 150 T B mate1 technical by mapping diff illumina novaseq_era unknown poly_a unknown sc single_cell_droplet 10x   China 2023-05-25 Larval Larval Liver Liver and Biliary 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");;