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run_metadata

6 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "size fractionation" and tissue_curation = "Heart"

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tissue_curation_coarse 1

tissue_curation 1

  • Heart · 6 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 6 ✖

experiment.library_layout 1

  • PAIRED · 6 ✖

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
42495 42495 SRR5666979 SRX2902577 SRS2269173 SRP108989 PRJNA390119 HLX & Hematopoiesis PRJNA390119 Other HLX &amp; Hematopoiesis     rnaseq and atacseq hlx hematopoiesis hlx   isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal                 kdrl GFP cells hlx1 MO rep2 3 kdrl GFP cells hlx1 MO rep2 SMART SEQ ultra low RNA seq kit Clonetech     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP108989   assembly:danRer10 flk_gfp_hlx_8ng_48hrs_2_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_2_R2.fastq.gz fastq fastq 1887289200.0 12581928.0 flk gfp hlx 8ng 48hrs 2 R1.fastq.gz 0:75 1:75 A:493825524;C:448630716;G:436118597;T:508410442;N:303921 75 75     493825524 448630716 436118597 508410442 303921 SRX2902577 SRS2269173 SRA573518 BRFAA|Molecular Biology BRFAA 2 0.9202 0.9216 0.09499 0.09558 0.73805 0.73878 0.48809 0.48787 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Greece 2017-06-13 Undetermined Undetermined Heart Cardiovascular System
42496 42496 SRR5666980 SRX2902576 SRS2269173 SRP108989 PRJNA390119 HLX & Hematopoiesis PRJNA390119 Other HLX &amp; Hematopoiesis     rnaseq and atacseq hlx hematopoiesis hlx   isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal                 kdrl GFP cells hlx1 MO rep1 2 kdrl GFP cells hlx1 MO rep1 SMART SEQ ultra low RNA seq kit Clonetech     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP108989   assembly:danRer10 flk_gfp_hlx_8ng_48hrs_1_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_1_R2.fastq.gz fastq fastq 1561083900.0 10407226.0 flk gfp hlx 8ng 48hrs 1 R2.fastq.gz 0:75 1:75 A:412744284;C:366776465;G:356834742;T:424473871;N:254538 75 75     412744284 366776465 356834742 424473871 254538 SRX2902576 SRS2269173 SRA573518 BRFAA|Molecular Biology BRFAA 2 0.9172 0.91824 0.09957 0.09961 0.73965 0.73975 0.48906 0.48977 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Greece 2017-06-13 Undetermined Undetermined Heart Cardiovascular System
42497 42497 SRR5666981 SRX2902575 SRS2269173 SRP108989 PRJNA390119 HLX & Hematopoiesis PRJNA390119 Other HLX &amp; Hematopoiesis     rnaseq and atacseq hlx hematopoiesis hlx   isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal                 kdrl GFP cells control 2 1 kdrl GFP cells control 2 SMART SEQ ultra low RNA seq kit Clonetech     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP108989   assembly:danRer10 flk_gfp_48hrs_con2_R1.fastq.gz flk_gfp_48hrs_con2_R2.fastq.gz fastq fastq 2042164500.0 13614430.0 flk gfp 48hrs con2 R1.fastq.gz 0:75 1:75 A:537008617;C:483956616;G:465380092;T:555490621;N:328554 75 75     537008617 483956616 465380092 555490621 328554 SRX2902575 SRS2269173 SRA573518 BRFAA|Molecular Biology BRFAA 2 0.91492 0.91762 0.10575 0.10669 0.75519 0.75546 0.49482 0.49617 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Greece 2017-06-13 Undetermined Undetermined Heart Cardiovascular System
42498 42498 SRR5666982 SRX2902574 SRS2269173 SRP108989 PRJNA390119 HLX & Hematopoiesis PRJNA390119 Other HLX &amp; Hematopoiesis     rnaseq and atacseq hlx hematopoiesis hlx   isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal                 kdrl GFP cells control 1 0 kdrl GFP cells control 1 SMART SEQ ultra low RNA seq kit Clonetech     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP108989   assembly:danRer10 flk_gfp_48hrs_con1_R2.fastq.gz flk_gfp_48hrs_con1_R1.fastq.gz fastq fastq 1678987200.0 11193248.0 flk gfp 48hrs con1 R2.fastq.gz 0:75 1:75 A:437283407;C:401234553;G:387947515;T:452257282;N:264443 75 75     437283407 401234553 387947515 452257282 264443 SRX2902574 SRS2269173 SRA573518 BRFAA|Molecular Biology BRFAA 2 0.91593 0.91737 0.08937 0.08988 0.75607 0.75696 0.50103 0.45539 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Greece 2017-06-13 Undetermined Undetermined Heart Cardiovascular System
42499 42499 SRR5666985 SRX2902571 SRS2269173 SRP108989 PRJNA390119 HLX & Hematopoiesis PRJNA390119 Other HLX &amp; Hematopoiesis     rnaseq and atacseq hlx hematopoiesis hlx   isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal                 fli GFP cells hHLXOE rep 2 5 fli GFP cells hHLXOE rep 2 SMART SEQ ultra low RNA seq kit Clonetech     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP108989   assembly:danRer10 fli_gal4_uas_hlx_endo_48h_s2_R2.fastq.gz fli_gal4_uas_hlx_endo_48h_s2_R1.fastq.gz fastq fastq 4490898450.0 29939323.0 fli gal4 uas hlx endo 48h s2 R2.fastq.gz 0:75 1:75 A:870349076;C:1346136891;G:1401796534;T:869066463;N:3549486 75 75     870349076 1346136891 1401796534 869066463 3549486 SRX2902571 SRS2269173 SRA573518 BRFAA|Molecular Biology BRFAA 2 0.5714 0.57344 0.27957 0.28321 0.85102 0.85342 0.53304 0.53368 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Greece 2017-06-13 Undetermined Undetermined Heart Cardiovascular System
42500 42500 SRR5666986 SRX2902570 SRS2269173 SRP108989 PRJNA390119 HLX & Hematopoiesis PRJNA390119 Other HLX &amp; Hematopoiesis     rnaseq and atacseq hlx hematopoiesis hlx   isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal                 fli GFP cells hHLXOE rep 1 4 fli GFP cells hHLXOE rep 1 SMART SEQ ultra low RNA seq kit Clonetech     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP108989   assembly:danRer10 fli_gal4_uas_hlx_endo_48h_s1_R1.fastq.gz fli_gal4_uas_hlx_endo_48h_s1_R2.fastq.gz fastq fastq 3459602100.0 23064014.0 fli gal4 uas hlx endo 48h s1 R1.fastq.gz 0:75 1:75 A:658343595;C:1050309687;G:1097759573;T:650443491;N:2745754 75 75     658343595 1050309687 1097759573 650443491 2745754 SRX2902570 SRS2269173 SRA573518 BRFAA|Molecular Biology BRFAA 2 0.57077 0.57481 0.2173 0.2185 0.79553 0.79762 0.50405 0.48708 75 75 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Greece 2017-06-13 Undetermined Undetermined Heart Cardiovascular 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");;