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run_metadata

5 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "RANDOM" and technology = "generic-scrnaseq-only"

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tissue_curation_coarse 2

tissue_curation 2

devstage_curation_coarse 2

devstage_curation 2

technology 1

  • generic-scrnaseq-only · 5 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 5 ✖

experiment.library_layout 1

  • PAIRED · 5 ✖
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
34262 34262 SRR31595085 SRX26959911 SRS23429841 SRP549196 PRJNA1193812 Single cell transcriptome sequencing of zebrafish olfactory epithelium PRJNA1193812 Other We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.     Alarm substances treatment Group   CAS   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 year old|dev stage:adult CAS group|collection date:2020 10 10|geo loc name:China: Wuhan|sex:male|tissue:Olfactory epithelium CAS group|BioSampleModel:Model organism or animal                 Single cell transcriptome of the AB zebrafish olfactory epithelium post treatment with alarm substances CAS OE CAS OE sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA NextSeq 550   SRP549196     CAS_S1_L001_R1_001.fastq.gz CAS_S1_L001_R2_001.fastq.gz fastq fastq 54518124857.0 458135503.0 CAS S1 L001 R1 001.fastq.gz 0:28 1:91 A:15384916510;C:12274547586;G:14008767028;T:12837270924;N:12622809 28 91     15384916510 12274547586 14008767028 12837270924 12622809 SRX26959911 SRS23429841 SRA2027027 Institute of Hydrobiology, Chinese Academy of Sciences|Chinese Academy of Sciences Institute of Hydrobiology, Chinese Academy of Sciences                       T B sc-like readlen illumina nextseq unknown random_priming unknown sc single_cell_generic generic-scrnaseq-only   China 2024-12-04 Adult Adult Brain Nervous System
34263 34263 SRR31595086 SRX26959910 SRS23429840 SRP549196 PRJNA1193812 Single cell transcriptome sequencing of zebrafish olfactory epithelium PRJNA1193812 Other We performed single cell sequencing in the olfactory epithelium of wild type zebrafish and zebrafish treated with alarm substances and compared them.     Blank control group   CTR   strain:AB strain|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:1 year old|dev stage:adult CTR group|collection date:2020 10 10|geo loc name:China: Wuhan|sex:male|tissue:Olfactory epithelium CTR group|BioSampleModel:Model organism or animal                 Single cell transcriptome of the AB strain zebrafish olfactory epithelium CTR OE CTR OE sequencing libraries were loaded on an Illumina NextSeq 550AR with paired end kits. Read 1 was used to distinguish different transcripts of different cells. Read 2 was used to determine the genetic information.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA NextSeq 550   SRP549196     CTR_S1_L001_R1_001.fastq.gz CTR_S1_L001_R2_001.fastq.gz fastq fastq 50773421790.0 426667410.0 CTR S1 L001 R1 001.fastq.gz 0:28 1:91 A:14105926130;C:11510784907;G:13135577448;T:12011516484;N:9616821 28 91     14105926130 11510784907 13135577448 12011516484 9616821 SRX26959910 SRS23429840 SRA2027027 Institute of Hydrobiology, Chinese Academy of Sciences|Chinese Academy of Sciences Institute of Hydrobiology, Chinese Academy of Sciences                       T B sc-like readlen illumina nextseq unknown random_priming unknown sc single_cell_generic generic-scrnaseq-only   China 2024-12-04 Adult Adult Brain Nervous System
68777 68777 SRR18188990 SRX14335888 SRS12150682 SRP362100 PRJNA811725 Single cell sequencing of zebra fish primordial germ cell PRJNA811725 Other Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.         GC9   strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube|age:5hpf|dev stage:30% 50% epiboly|sex:not applicable|tissue:primordial germ cell|cell type:primordial germ cell|replicate:replicate3|BioSampleModel:Model organism or animal                 3pgc 3 3pgc 3 3pgc primordial germ cell from 5 hpf zebrafish embryos     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP362100     GC9_R1.fq.gz GC9_R2.fq.gz fastq fastq 16392678600.0 54642262.0 GC9 R1.fq.gz 0:150 1:150 A:4548403510;C:3786937912;G:3801036342;T:4255236177;N:1064659 150 150     4548403510 3786937912 3801036342 4255236177 1064659 SRX14335888 SRS12150682 SRA1379556 Sun-Yat sen University|School of Marine Science Sun-Yat sen University 2 0.92711 0.93044 0.08622 0.08652 0.79693 0.80306 0.58096 0.58168 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown sc single_cell_generic generic-scrnaseq-only   China 2022-03-02 Multi-stage Embryo Gonad Reproductive System
68778 68778 SRR18188991 SRX14335887 SRS12150683 SRP362100 PRJNA811725 Single cell sequencing of zebra fish primordial germ cell PRJNA811725 Other Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.         GC4   strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube|age:5hpf|dev stage:30% 50% epiboly|sex:not applicable|tissue:primordial germ cell|cell type:primordial germ cell|replicate:replicate2|BioSampleModel:Model organism or animal                 2pgc 2 2pgc 2 2pgc primordial germ cell from 5 hpf zebrafish embryos     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP362100     GC4_R1.fq.gz GC4_R2.fq.gz fastq fastq 14471348700.0 48237829.0 GC4 R1.fq.gz 0:150 1:150 A:4127039158;C:3211803959;G:3224340004;T:3907215356;N:950223 150 150     4127039158 3211803959 3224340004 3907215356 950223 SRX14335887 SRS12150683 SRA1379556 Sun-Yat sen University|School of Marine Science Sun-Yat sen University 2 0.91951 0.91886 0.14001 0.14043 0.75777 0.76605 0.55643 0.55313 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown sc single_cell_generic generic-scrnaseq-only   China 2022-03-02 Multi-stage Embryo Gonad Reproductive System
68779 68779 SRR18188992 SRX14335886 SRS12150681 SRP362100 PRJNA811725 Single cell sequencing of zebra fish primordial germ cell PRJNA811725 Other Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.         GC1   strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube|age:5hpf|dev stage:30% 50% epiboly|sex:not applicable|tissue:primordial germ cell|cell type:primordial germ cell|replicate:replicate1|BioSampleModel:Model organism or animal                 1pgc 1 1pgc 1 1pgc primordial germ cell from 5 hpf zebrafish embryos     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP362100     GC1_R1.fq.gz GC1_R2.fq.gz fastq fastq 18801698100.0 62672327.0 GC1 R1.fq.gz 0:150 1:150 A:5242992703;C:4310290517;G:4334163362;T:4913025193;N:1226325 150 150     5242992703 4310290517 4334163362 4913025193 1226325 SRX14335886 SRS12150681 SRA1379556 Sun-Yat sen University|School of Marine Science Sun-Yat sen University 2 0.93192 0.93277 0.09532 0.09559 0.78358 0.7906 0.5661 0.56344 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown sc single_cell_generic generic-scrnaseq-only   China 2022-03-02 Multi-stage Embryo Gonad Reproductive 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");;