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run_metadata

8 rows where devstage_curation = "Juvenile" and experiment.library_strategy = "AMPLICON"

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tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • AMPLICON · 8 ✖

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

  • Juvenile · 8 ✖
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
68297 68297 SRR099352 SRX041562 SRS172412 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode CTCGCGTGTC 4433 1MA D8 4433 1MA D8                     1 4433 1MA D8 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         70233197.0 233302.0 4433 1MA D8 0:4 1:297.04   4 297               SRX041562 SRS172412 SRA029829 Stanford University|Quake Stanford University 1 0.14812   0.01088   0.99969   0.10799   36   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68298 68298 SRR099351 SRX041561 SRS172411 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode CGTGTCTCTA 4433 1MA C7 4433 1MA C7                     1 4433 1MA C7 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         109094731.0 316792.0 4433 1MA C7 0:4 1:340.37   4 340               SRX041561 SRS172411 SRA029829 Stanford University|Quake Stanford University 1 0.13409   0.01258   0.99955   0.01535   37   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68299 68299 SRR099350 SRX041560 SRS172410 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode ATATCGCGAG 4433 1MA B6 4433 1MA B6                     1 4433 1MA B6 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         110436791.0 353780.0 4433 1MA B6 0:4 1:308.16   4 308               SRX041560 SRS172410 SRA029829 Stanford University|Quake Stanford University 1 0.28629   0.01104   0.99945   0.0273   107   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68300 68300 SRR099349 SRX041559 SRS172409 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode ATCAGACACG 4433 1MA A5 4433 1MA A5                     1 4433 1MA A5 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         107336405.0 335816.0 4433 1MA A5 0:4 1:315.63   4 315               SRX041559 SRS172409 SRA029829 Stanford University|Quake Stanford University 1 0.16203   0.01649   0.99935   0.00111   37   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68301 68301 SRR099329 SRX041558 SRS172408 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode AGCACTGTAG 4432 1MA D4 4432 1MA D4                     1 4432 1MA D4 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         94113837.0 297721.0 4432 1MA D4 0:4 1:312.11   4 312               SRX041558 SRS172408 SRA029829 Stanford University|Quake Stanford University 1 0.16753   0.02013   0.99979   3e-05   37   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68302 68302 SRR099328 SRX041557 SRS172407 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode AGACGCACTC 4432 1MA C3 4432 1MA C3                     1 4432 1MA C3 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         77768777.0 243405.0 4432 1MA C3 0:4 1:315.50   4 315               SRX041557 SRS172407 SRA029829 Stanford University|Quake Stanford University 1 0.16711   0.01816   0.99979   0.0   37   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68303 68303 SRR099327 SRX041556 SRS172406 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode ACGCTCGACA 4432 1MA B2 4432 1MA B2                     1 4432 1MA B2 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         120450312.0 390504.0 4432 1MA B2 0:4 1:304.45   4 304               SRX041556 SRS172406 SRA029829 Stanford University|Quake Stanford University 1 0.18757   0.01811   0.99977   0.00024   59   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68304 68304 SRR099326 SRX041555 SRS172405 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode ACGAGTGCGT 4432 1MA A1 4432 1MA A1                     1 4432 1MA A1 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         145945736.0 457354.0 4432 1MA A1 0:4 1:315.11   4 315               SRX041555 SRS172405 SRA029829 Stanford University|Quake Stanford University 1 0.17607   0.02473   0.99957   0.00036   40   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic 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");;