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run_metadata

8 rows where devstage_curation_coarse = "Larval" and tissue_curation = "BCR TCR repertoire"

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tissue_curation_coarse 1

tissue_curation 1

  • BCR TCR repertoire · 8 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

  • Larval · 8 ✖

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
68305 68305 SRR099356 SRX041554 SRS172404 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 2 wpf WIK zebrafish Danio rerio leading with MID barcode CTCGCGTGTC 4433 2WD 4433 2WD                     1 4433 2WD 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     4433-2WDqual.tar.gz fastq 52787937.0 159839.0 4433 2WD 0:4 1:326.26   4 326               SRX041554 SRS172404 SRA029829 Stanford University|Quake Stanford University 1 0.11986   0.01724   0.99805   0.01122   313   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-08 Larval Larval BCR TCR repertoire Hematopoietic System
68306 68306 SRR099355 SRX041553 SRS172403 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 2 wpf WIK zebrafish Danio rerio leading with MID barcode CGTGTCTCTA 4433 2WC 4433 2WC                     1 4433 2WC 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         65896148.0 208053.0 4433 2WC 0:4 1:312.73   4 312               SRX041553 SRS172403 SRA029829 Stanford University|Quake Stanford University 1 0.14138   0.02922   0.99855   0.00348   315   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Larval Larval BCR TCR repertoire Hematopoietic System
68307 68307 SRR099354 SRX041552 SRS172402 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 2 wpf WIK zebrafish Danio rerio leading with MID barcode ATATCGCGAG 4433 2WB 4433 2WB                     1 4433 2WB 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         63865512.0 209572.0 4433 2WB 0:4 1:300.74   4 300               SRX041552 SRS172402 SRA029829 Stanford University|Quake Stanford University 1 0.16321   0.03058   0.99926   0.00107   226   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Larval Larval BCR TCR repertoire Hematopoietic System
68308 68308 SRR099353 SRX041551 SRS172401 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 2 wpf WIK zebrafish Danio rerio leading with MID barcode ATCAGACACG 4433 2WA 4433 2WA                     1 4433 2WA 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         41165356.0 128188.0 4433 2WA 0:4 1:317.13   4 317               SRX041551 SRS172401 SRA029829 Stanford University|Quake Stanford University 1 0.16018   0.02829   0.99847   0.02343   452   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Larval Larval BCR TCR repertoire Hematopoietic System
68309 68309 SRR099337 SRX041550 SRS172400 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 2 wpf WIK zebrafish Danio rerio leading with MID barcode AGCACTGTAG 4432 2WD 4432 2WD                     1 4432 2WD 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         34384017.0 109589.0 4432 2WD 0:4 1:309.75   4 309               SRX041550 SRS172400 SRA029829 Stanford University|Quake Stanford University 1 0.1533   0.02541   0.99896   0.00428   254   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Larval Larval BCR TCR repertoire Hematopoietic System
68310 68310 SRR099336 SRX041549 SRS172399 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 2 wpf WIK zebrafish Danio rerio leading with MID barcode AGACGCACTC 4432 2WC 4432 2WC                     1 4432 2WC 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         71040021.0 233525.0 4432 2WC 0:4 1:300.21   4 300               SRX041549 SRS172399 SRA029829 Stanford University|Quake Stanford University 1 0.16787   0.03447   0.9978   0.01646   360   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Larval Larval BCR TCR repertoire Hematopoietic System
68311 68311 SRR099335 SRX041548 SRS172345 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 2 wpf WIK zebrafish Danio rerio leading with MID barcode ACGCTCGACA 4432 2WB 4432 2WB                     1 4432 2WB 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         98153866.0 302470.0 4432 2WB 0:4 1:320.51   4 320               SRX041548 SRS172345 SRA029829 Stanford University|Quake Stanford University 1 0.15713   0.047   0.99774   0.02379   137   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Larval Larval BCR TCR repertoire Hematopoietic System
68312 68312 SRR099334 SRX041547 SRS172117 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 2 wpf WIK zebrafish Danio rerio leading with MID barcode ACGAGTGCGT 4432 2WA 4432 2WA                     1 4432 2WA 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         91079672.0 319475.0 4432 2WA 0:4 1:281.09   4 281               SRX041547 SRS172117 SRA029829 Stanford University|Quake Stanford University 1 0.25569   0.04646   0.99902   0.00137   88   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Larval Larval 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");;