RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

3 rows where experiment.library_selection = "RANDOM", technology = "generic-scrnaseq-only" and tissue_curation_coarse = "Reproductive System"

✎ View and edit SQL

This data as json, CSV (advanced)

tissue_curation_coarse 1

  • Reproductive System · 3 ✖

tissue_curation 1

technology 1

  • generic-scrnaseq-only · 3 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 3 ✖

experiment.library_layout 1

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
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

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

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");;