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run_metadata

10 rows where devstage_curation = "Juvenile" and tissue_curation_coarse = "Undetermined"

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experiment.library_selection 2

tissue_curation_coarse 1

  • Undetermined · 10 ✖

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Juvenile · 10 ✖
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
41248 41248 SRR3985378 SRX1987647 SRS1591650 SRP080226 PRJNA335774 wt vs mutant zebrafish Raw sequence reads PRJNA335774 Other be related to IS     mutant Stat3 zebrafish Stat3   strain:AB line|age:1 month|dev stage:juvenile fish|sex:not determined|tissue:b1|biomaterial provider:nstitute of hydrobiology|treatment:KO|BioSampleModel:Model organism or animal                 stat3 mutant stat3 mutant 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>4000</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>2001</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP080226     Stat3_1.fq.gz Stat3_2.fq.gz fastq fastq 8539658400.0 28465528.0 stat3 mutant 0:150 1:150 A:2247683479;C:2023626545;G:2038225527;T:2229672357;N:450492 150 150     2247683479 2023626545 2038225527 2229672357 450492 SRX1987647 SRS1591650 SRA445588 Huazhong Agricultural University Huazhong Agricultural University 2 0.88446 0.81717 0.0523 0.04777 0.69887 0.70642 0.45266 0.49099 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2017-01-18 Juvenile Juvenile Undetermined Undetermined
41249 41249 SRR3985375 SRX1987645 SRS1591255 SRP080226 PRJNA335774 wt vs mutant zebrafish Raw sequence reads PRJNA335774 Other be related to IS     wild type   wild type zebrafish   strain:AB|age:1 month|dev stage:juvenile fish|sex:not determined|tissue:b1|BioSampleModel:Model organism or animal                 wild type zebrafish wild type control 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>4000</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>2001</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP080226     WT-1_1.fq.gz WT-1_2.fq.gz fastq fastq 8539964400.0 28466548.0 wild type control 0:150 1:150 A:2252816933;C:2019884847;G:2037382553;T:2229414884;N:465183 150 150     2252816933 2019884847 2037382553 2229414884 465183 SRX1987645 SRS1591255 SRA445586 Huazhong Agricultural University Huazhong Agricultural University 2 0.88395 0.81555 0.05189 0.04746 0.69134 0.69921 0.4902 0.49597 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2017-01-18 Juvenile Juvenile Undetermined Undetermined
41509 41509 SRR4994225 SRX2329687 SRS1591255 SRP092647 PRJNA352610 Danio rerio strain:AB Raw sequence reads PRJNA352610 Whole Genome Sequencing wild type     wild type   wild type zebrafish   strain:AB|age:1 month|dev stage:juvenile fish|sex:not determined|tissue:b1|BioSampleModel:Model organism or animal                 wild type wild type zebrafish 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>4000</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>2001</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP092647         8539964400.0 28466548.0 wild type zebrafish 0:150 1:150 A:2252816933;C:2019884847;G:2037382553;T:2229414884;N:465183 150 150     2252816933 2019884847 2037382553 2229414884 465183 SRX2329687 SRS1591255 SRA490795 Huazhong Agricultural University Huazhong Agricultural University 2 0.88393 0.81554 0.05185 0.04727 0.69138 0.69905 0.49044 0.49588 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2016-11-07 Juvenile Juvenile Undetermined Undetermined
41510 41510 SRR4994317 SRX2329715 SRS1591650 SRP092650 PRJNA352611 Danio rerio strain:AB Raw sequence reads PRJNA352611 Whole Genome Sequencing provide a clue for studying congenital scoliosis desease     mutant Stat3 zebrafish Stat3   strain:AB line|age:1 month|dev stage:juvenile fish|sex:not determined|tissue:b1|biomaterial provider:nstitute of hydrobiology|treatment:KO|BioSampleModel:Model organism or animal                 stat3 mutant stat3 1 1     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>4000</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>2001</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP092650         8539658400.0 28465528.0 stat3 0:150 1:150 A:2247683479;C:2023626545;G:2038225527;T:2229672357;N:450492 150 150     2247683479 2023626545 2038225527 2229672357 450492 SRX2329715 SRS1591650 SRA490799 Huazhong Agricultural University Huazhong Agricultural University 2 0.88451 0.81718 0.05225 0.0476 0.69885 0.7065 0.48442 0.49075 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2016-11-07 Juvenile Juvenile Undetermined Undetermined
68548 68548 SRR18056674 SRX14208687 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT6 6 6 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT6.R1.fq.gz SS3WT6.R2.fq.gz fastq fastq 7174164397.0 25400980.0 SS3WT6.R1.fq.gz 0:141.31 1:141.13 A:1934605412;C:1644763885;G:1664938935;T:1929811138;N:45027 141 141     1934605412 1644763885 1664938935 1929811138 45027 SRX14208687 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94928 0.94948 0.09187 0.09099 0.68765 0.68769 0.50435 0.50363 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68549 68549 SRR18056675 SRX14208686 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT5 5 5 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT5.R1.fq.gz SS3WT5.R2.fq.gz fastq fastq 7159028081.0 25133913.0 SS3WT5.R1.fq.gz 0:142.50 1:142.33 A:1905921436;C:1664337487;G:1683294939;T:1905427825;N:46394 142 142     1905921436 1664337487 1683294939 1905427825 46394 SRX14208686 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94917 0.95027 0.09384 0.09347 0.6594 0.65894 0.49218 0.49202 122 122 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68550 68550 SRR18056676 SRX14208685 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT4 4 4 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT4.R1.fq.gz SS3WT4.R2.fq.gz fastq fastq 6985092696.0 24360978.0 SS3WT4.R1.fq.gz 0:143.44 1:143.29 A:1858629258;C:1624045323;G:1642960060;T:1859412787;N:45268 143 143     1858629258 1624045323 1642960060 1859412787 45268 SRX14208685 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94221 0.94208 0.1047 0.1038 0.66231 0.66251 0.49213 0.49128 113 112 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68551 68551 SRR18056677 SRX14208684 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT3 3 3 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT3.R1.fq.gz SS3WT3.R2.fq.gz fastq fastq 6604271936.0 23189546.0 SS3WT3.R1.fq.gz 0:142.47 1:142.32 A:1765899330;C:1527534084;G:1543609939;T:1767186572;N:42011 142 142     1765899330 1527534084 1543609939 1767186572 42011 SRX14208684 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94017 0.94088 0.10254 0.10225 0.65163 0.65167 0.47798 0.47707 131 131 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68552 68552 SRR18056678 SRX14208683 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT2 2 2 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT2.R1.fq.gz SS3WT2.R2.fq.gz fastq fastq 6674317073.0 23265242.0 SS3WT2.R1.fq.gz 0:143.52 1:143.36 A:1768071045;C:1560492667;G:1576548690;T:1769161220;N:43451 143 143     1768071045 1560492667 1576548690 1769161220 43451 SRX14208683 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94677 0.9473 0.08956 0.08902 0.66559 0.66557 0.48058 0.48136 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined
68553 68553 SRR18056679 SRX14208682 SRS12030730 SRP360305 PRJNA806354 Danio rerio Raw sequence reads PRJNA806354 Whole Genome Sequencing Danio rerio RNA seq reads       Model organism or animal sample from Danio rerio sample 001   breed:AB|age:50dpf|sex:not collected|tissue:b1|BioSampleModel:Model organism or animal                 SS3WT1 1 1 commen method     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP360305     SS3WT1.R1.fq.gz SS3WT1.R2.fq.gz fastq fastq 6848211264.0 23787995.0 SS3WT1.R1.fq.gz 0:144.06 1:143.82 A:1825907736;C:1587014566;G:1607121352;T:1828122105;N:45505 144 143     1825907736 1587014566 1607121352 1828122105 45505 SRX14208682 SRS12030730 SRA1373545 Shanghai Ocean University|College of Fisheries and life Shanghai Ocean University 2 0.94226 0.94255 0.09053 0.08971 0.65807 0.65823 0.48525 0.48427 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2022-02-22 Juvenile Juvenile Undetermined Undetermined

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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");;