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run_metadata

6 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation = "Thymus"

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tissue_curation_coarse 1

tissue_curation 1

  • Thymus · 6 ✖

technology 1

  • unknown · 6 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

  • SINGLE · 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
59579 59579 SRR11926625 SRX8472271 SRS6772872 SRP265974 PRJNA637328 A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models GSE151816 Transcriptome Analysis We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes   pubmed:32591643   AB thymus 9 GSM4591306   tissue:Healthy dissected thymus|cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab AB thymus 9 First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts Healthy dissected thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab GSM4591306 GSM4591306: AB thymus 9; Danio rerio; RNA Seq GSM4591306   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591306 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP265974     sample_6.fastq.gz fastq 2786385619.0 36888152.0 GSM4591306 r1 0:75.54 1:0 A:663089588;C:692060734;G:651825670;T:779197417;N:212210 75 0     663089588 692060734 651825670 779197417 212210 SRX8472271 SRS6772872 SRA1083220 GEO Center for Medical Genetics, Ghent University 1 0.94942   0.05717   0.73018   0.49009   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59580 59580 SRR11926624 SRX8472270 SRS6772871 SRP265974 PRJNA637328 A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models GSE151816 Transcriptome Analysis We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes   pubmed:32591643   AB thymus 8 GSM4591305   tissue:Healthy dissected thymus|cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab AB thymus 8 First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts Healthy dissected thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab GSM4591305 GSM4591305: AB thymus 8; Danio rerio; RNA Seq GSM4591305   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591305 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP265974     sample_5.fastq.gz fastq 2456067469.0 32519095.0 GSM4591305 r1 0:75.53 1:0 A:606304745;C:594426559;G:556316196;T:698842180;N:177789 75 0     606304745 594426559 556316196 698842180 177789 SRX8472270 SRS6772871 SRA1083220 GEO Center for Medical Genetics, Ghent University 1 0.94282   0.08874   0.70851   0.49253   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59581 59581 SRR11926623 SRX8472269 SRS6772870 SRP265974 PRJNA637328 A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models GSE151816 Transcriptome Analysis We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes   pubmed:32591643   AB thymus 7 GSM4591304   tissue:Healthy dissected thymus|cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab AB thymus 7 First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts Healthy dissected thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab GSM4591304 GSM4591304: AB thymus 7; Danio rerio; RNA Seq GSM4591304   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591304 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP265974     sample_4.fastq.gz fastq 2889915115.0 38259114.0 GSM4591304 r1 0:75.54 1:0 A:694082728;C:713330573;G:669832103;T:812454853;N:214858 75 0     694082728 713330573 669832103 812454853 214858 SRX8472269 SRS6772870 SRA1083220 GEO Center for Medical Genetics, Ghent University 1 0.94794   0.06446   0.72697   0.49962   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59582 59582 SRR11926622 SRX8472268 SRS6772869 SRP265974 PRJNA637328 A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models GSE151816 Transcriptome Analysis We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes   pubmed:32591643   AB thymus 2 3 5 6 GSM4591303   tissue:Healthy dissected thymus|cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab AB thymus 2 3 5 6 First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts Healthy dissected thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab GSM4591303 GSM4591303: AB thymus 2 3 5 6; Danio rerio; RNA Seq GSM4591303   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591303 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP265974     sample_3.fastq.gz fastq 2338535479.0 30955998.0 GSM4591303 r1 0:75.54 1:0 A:540165709;C:595429439;G:553807340;T:648952381;N:180610 75 0     540165709 595429439 553807340 648952381 180610 SRX8472268 SRS6772869 SRA1083220 GEO Center for Medical Genetics, Ghent University 1 0.94992   0.04962   0.73032   0.4837   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59583 59583 SRR11926621 SRX8472267 SRS6772868 SRP265974 PRJNA637328 A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models GSE151816 Transcriptome Analysis We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes   pubmed:32591643   AB thymus 11 GSM4591302   tissue:Healthy dissected thymus|cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab AB thymus 11 First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts Healthy dissected thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab GSM4591302 GSM4591302: AB thymus 11; Danio rerio; RNA Seq GSM4591302   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591302 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP265974     sample_2.fastq.gz fastq 2942053849.0 38949737.0 GSM4591302 r1 0:75.53 1:0 A:688398915;C:734856328;G:694653408;T:823920342;N:224856 75 0     688398915 734856328 694653408 823920342 224856 SRX8472267 SRS6772868 SRA1083220 GEO Center for Medical Genetics, Ghent University 1 0.94862   0.06975   0.72224   0.49305   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59584 59584 SRR11926620 SRX8472266 SRS6772867 SRP265974 PRJNA637328 A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models GSE151816 Transcriptome Analysis We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes   pubmed:32591643   AB thymus 10 GSM4591301   tissue:Healthy dissected thymus|cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab AB thymus 10 First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts Healthy dissected thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tgrag2:GFP|tumor stg:healthy|lab of sample collection and sequencing:Speleman lab GSM4591301 GSM4591301: AB thymus 10; Danio rerio; RNA Seq GSM4591301   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591301 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP265974     sample_1.fastq.gz fastq 2923525817.0 38707354.0 GSM4591301 r1 0:75.53 1:0 A:697204107;C:721945575;G:689048693;T:815100976;N:226466 75 0     697204107 721945575 689048693 815100976 226466 SRX8472266 SRS6772867 SRA1083220 GEO Center for Medical Genetics, Ghent University 1 0.94964   0.05377   0.71904   0.4902   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus 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");;