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run_metadata

9 rows where experiment.library_layout = "PAIRED", technology = "generic-scrnaseq-only" and tissue_curation = "Undetermined"

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devstage_curation 3

tissue_curation_coarse 1

tissue_curation 1

  • Undetermined · 9 ✖

technology 1

  • generic-scrnaseq-only · 9 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

  • PAIRED · 9 ✖

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
50535 50535 SRR8134458 SRX4955494 SRS3996631 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H24 3   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 3|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H24 3 H24 3 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H24_3_R1.fastq H24_3_R2.fastq fastq fastq 1303220750.0 5212883.0 H24 3 R1.fastq 0:125 1:125 A:353042196;C:298548859;G:299882991;T:351742904;N:3800 125 125     353042196 298548859 299882991 351742904 3800 SRX4955494 SRS3996631 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.95284 0.94903 0.03485 0.03522 0.8606 0.86168 0.49556 0.49795 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Pharyngula Embryo Undetermined Embryo Imprecise
50536 50536 SRR8134459 SRX4955493 SRS3996630 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H24 1   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 1|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H24 1 H24 1 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H24_1_R1.fastq H24_1_R2.fastq fastq fastq 1040367750.0 4161471.0 H24 1 R1.fastq 0:125 1:125 A:285190807;C:235796611;G:237165817;T:282211556;N:2959 125 125     285190807 235796611 237165817 282211556 2959 SRX4955493 SRS3996630 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94648 0.94488 0.0507 0.05253 0.87353 0.87513 0.52936 0.52764 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Pharyngula Embryo Undetermined Embryo Imprecise
50537 50537 SRR8134460 SRX4955492 SRS3996629 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H24 2   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:24hpf biological replicate 2|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H24 2 H24 2 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H24_2_R1.fastq H24_2_R2.fastq fastq fastq 1003243000.0 4012972.0 H24 2 R1.fastq 0:125 1:125 A:275192369;C:227024454;G:228346661;T:272676506;N:3010 125 125     275192369 227024454 228346661 272676506 3010 SRX4955492 SRS3996629 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94467 0.94348 0.06361 0.06541 0.8423 0.84478 0.51257 0.51745 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Pharyngula Embryo Undetermined Embryo Imprecise
50538 50538 SRR8134461 SRX4955491 SRS3996628 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H11 2   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:11hpf biological replicate 2|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H11 2 H11 2 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H11_2_R1.fastq H11_2_R2.fastq fastq fastq 1034277500.0 4137110.0 H11 2 R1.fastq 0:125 1:125 A:286346530;C:232910512;G:234755237;T:280262966;N:2255 125 125     286346530 232910512 234755237 280262966 2255 SRX4955491 SRS3996628 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94693 0.94598 0.03067 0.03082 0.8562 0.85774 0.51961 0.51451 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Segmentation Embryo Undetermined Embryo Imprecise
50539 50539 SRR8134462 SRX4955490 SRS3996627 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H11 3   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:11hpf biological replicate 3|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H11 3 H11 3 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H11_3_R1.fastq H11_3_R2.fastq fastq fastq 1084328250.0 4337313.0 H11 3 R1.fastq 0:125 1:125 A:296459005;C:246835042;G:248291057;T:292740098;N:3048 125 125     296459005 246835042 248291057 292740098 3048 SRX4955490 SRS3996627 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.95199 0.95021 0.02101 0.02158 0.85914 0.86058 0.51593 0.41299 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Segmentation Embryo Undetermined Embryo Imprecise
50540 50540 SRR8134463 SRX4955489 SRS3996626 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H6 3   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:6hpf biological replicate 3|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H6 3 H6 3 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H6_3_R1.fastq H6_3_R2.fastq fastq fastq 989016500.0 3956066.0 H6 3 R1.fastq 0:125 1:125 A:270941686;C:224568911;G:226264637;T:267238750;N:2516 125 125     270941686 224568911 226264637 267238750 2516 SRX4955489 SRS3996626 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94889 0.94713 0.02757 0.02789 0.84415 0.84571 0.52218 0.52291 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Gastrula Embryo Undetermined Embryo Imprecise
50541 50541 SRR8134464 SRX4955488 SRS3996623 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H11 1   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:11hpf biological replicate 1|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H11 1 H11 1 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H11_1_R1.fastq H11_1_R2.fastq fastq fastq 707998500.0 2831994.0 H11 1 R1.fastq 0:125 1:125 A:194434087;C:160870744;G:162119289;T:190572787;N:1593 125 125     194434087 160870744 162119289 190572787 1593 SRX4955488 SRS3996623 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94561 0.94128 0.03328 0.03394 0.8589 0.86062 0.48582 0.48548 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Segmentation Embryo Undetermined Embryo Imprecise
50542 50542 SRR8134465 SRX4955487 SRS3996624 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H6 1   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:6hpf biological replicate 1|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H6 1 H6 1 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H6_1_R1.fastq H6_1_R2.fastq fastq fastq 759809500.0 3039238.0 H6 1 R1.fastq 0:125 1:125 A:211499426;C:170044275;G:171920878;T:206342561;N:2360 125 125     211499426 170044275 171920878 206342561 2360 SRX4955487 SRS3996624 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94965 0.94791 0.04309 0.04276 0.83485 0.83676 0.5519 0.56156 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Gastrula Embryo Undetermined Embryo Imprecise
50543 50543 SRR8134466 SRX4955486 SRS3996625 SRP167225 PRJNA501843 Characterization of Transcriptomic Profile in Early Zebrafish PGCs by Single Cell Sequencing PRJNA501843 Other Single cell RNA seq was applied for studying the transcriptomic profile in early zebrafish PGCsprimordial germ cells by choosing three time points during zebrafish embryonic development. The three time points were 6hpfhpf also called shield stage 11hpfalso called 3 somite stage and 24hpfalso called prim 5 stage.         H6 2   strain:AB|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|dev stage:6hpf biological replicate 2|sex:missing|tissue:PGC|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: PGC H6 2 H6 2 smart2     RNA-Seq TRANSCRIPTOMIC other PAIRED ILLUMINA Illumina HiSeq 2500   SRP167225     H6_2_R1.fastq H6_2_R2.fastq fastq fastq 858125000.0 3432500.0 H6 2 R1.fastq 0:125 1:125 A:236752508;C:193146437;G:194455657;T:233768197;N:2201 125 125     236752508 193146437 194455657 233768197 2201 SRX4955486 SRS3996625 SRA800727 Shanghai Institute of Biochemistry and Cell Biology, CAS|State Key Laboratory of cell Biology Shanghai Institute of Biochemistry and Cell Biology, CAS 2 0.94359 0.93966 0.04047 0.03943 0.83924 0.84396 0.54153 0.54602 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown sc_generic single_cell_generic generic-scrnaseq-only   China 2019-02-01 Gastrula Embryo Undetermined Embryo Imprecise

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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");;