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27 rows where technology = "unknown", tissue_curation = "Thymus" and tissue_curation_coarse = "Hematopoietic System"

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experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Hematopoietic System · 27 ✖

tissue_curation 1

  • Thymus · 27 ✖

technology 1

  • unknown · 27 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

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
59515 59515 SRR11926689 SRX8472335 SRS6772936 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   WT5 GSM4591370   tissue:Healthy sorted thymus|cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab WT5 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 sorted thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab GSM4591370 GSM4591370: WT5; Danio rerio; RNA Seq GSM4591370   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591370 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     FWTsample_5.fastq.gz FWTsample_5_R2.fastq.gz fastq fastq 4633582858.0 22938529.0 GSM4591370 r1 0:101 1:101 A:1263929939;C:1047240206;G:1052800791;T:1263574247;N:6037675 101 101     1263929939 1047240206 1052800791 1263574247 6037675 SRX8472335 SRS6772936 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.91347 0.91728 0.27187 0.27409 0.76585 0.76859 0.45662 0.48071 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59516 59516 SRR11926688 SRX8472334 SRS6772935 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   WT4 GSM4591369   tissue:Healthy sorted thymus|cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab WT4 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 sorted thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab GSM4591369 GSM4591369: WT4; Danio rerio; RNA Seq GSM4591369   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591369 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     FWTsample_4.fastq.gz FWTsample_4_R2.fastq.gz fastq fastq 4113149600.0 20565748.0 GSM4591369 r1 0:100 1:100 A:1084628064;C:963840734;G:985823964;T:1078691018;N:165820 100 100     1084628064 963840734 985823964 1078691018 165820 SRX8472334 SRS6772935 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.9336 0.93539 0.11919 0.11989 0.76368 0.76757 0.4904 0.47498 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59517 59517 SRR11926687 SRX8472333 SRS6772934 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   WT3 GSM4591368   tissue:Healthy sorted thymus|cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab WT3 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 sorted thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab GSM4591368 GSM4591368: WT3; Danio rerio; RNA Seq GSM4591368   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591368 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     FWTsample_3_R2.fastq.gz FWTsample_3.fastq.gz fastq fastq 3966667200.0 19833336.0 GSM4591368 r1 0:100 1:100 A:1125938234;C:857622800;G:856236104;T:1122434590;N:4435472 100 100     1125938234 857622800 856236104 1122434590 4435472 SRX8472333 SRS6772934 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.93918 0.92495 0.16292 0.15907 0.75866 0.76883 0.51794 0.51278 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59518 59518 SRR11926686 SRX8472332 SRS6772933 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   WT2 GSM4591367   tissue:Healthy sorted thymus|cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab WT2 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 sorted thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab GSM4591367 GSM4591367: WT2; Danio rerio; RNA Seq GSM4591367   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591367 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     FWTsample_2_R2.fastq.gz FWTsample_2.fastq.gz fastq fastq 3598961400.0 17994807.0 GSM4591367 r1 0:100 1:100 A:982353707;C:818188790;G:810911943;T:983465623;N:4041337 100 100     982353707 818188790 810911943 983465623 4041337 SRX8472332 SRS6772933 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.93426 0.9195 0.12591 0.12501 0.76763 0.77621 0.49491 0.50063 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59519 59519 SRR11926685 SRX8472331 SRS6772932 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   WT1 GSM4591366   tissue:Healthy sorted thymus|cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab WT1 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 sorted thymus   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab GSM4591366 GSM4591366: WT1; Danio rerio; RNA Seq GSM4591366   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591366 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     FWTsample_1_R2.fastq.gz FWTsample_1.fastq.gz fastq fastq 3686706000.0 18433530.0 GSM4591366 r1 0:100 1:100 A:1004954280;C:838347690;G:833756041;T:1005493425;N:4154564 100 100     1004954280 838347690 833756041 1005493425 4154564 SRX8472331 SRS6772932 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.93171 0.91783 0.13677 0.13606 0.76723 0.7752 0.51062 0.50949 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59520 59520 SRR11926684 SRX8472330 SRS6772931 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   SPL002 GSM4591365   tissue:shrek preleukemic thymocytes|cell type:thymocytes|genotype:shrek;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab SPL002 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 shrek preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:shrek;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591365 GSM4591365: SPL002; Danio rerio; RNA Seq GSM4591365   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591365 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_48.fastq.gz Fsample_48_R2.fastq.gz fastq fastq 23525993582.0 77900641.0 GSM4591365 r1 0:151 1:151 A:6365057472;C:5454588670;G:5620997543;T:6082859005;N:2490892 151 151     6365057472 5454588670 5620997543 6082859005 2490892 SRX8472330 SRS6772931 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.96011 0.96113 0.23076 0.22681 0.80858 0.81221 0.52577 0.51928 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59521 59521 SRR11926683 SRX8472329 SRS6772930 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   SPL001 GSM4591364   tissue:shrek preleukemic thymocytes|cell type:thymocytes|genotype:shrek;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab SPL001 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 shrek preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:shrek;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591364 GSM4591364: SPL001; Danio rerio; RNA Seq GSM4591364   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591364 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_47.fastq.gz Fsample_47_R2.fastq.gz fastq fastq 26795594770.0 88727135.0 GSM4591364 r1 0:151 1:151 A:7305822132;C:6082789601;G:6442162847;T:6961938191;N:2881999 151 151     7305822132 6082789601 6442162847 6961938191 2881999 SRX8472329 SRS6772930 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.96139 0.96343 0.22215 0.2185 0.81296 0.81647 0.50868 0.51446 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59532 59532 SRR11926672 SRX8472318 SRS6772919 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   OPL4 GSM4591353   tissue:otg preleukemic thymocytes|cell type:thymocytes|genotype:otg;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab OPL4 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 otg preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:otg;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591353 GSM4591353: OPL4; Danio rerio; RNA Seq GSM4591353   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591353 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_36.fastq.gz Fsample_36_R2.fastq.gz fastq fastq 4686865610.0 23202305.0 GSM4591353 r1 0:101 1:101 A:1290395271;C:1046629683;G:1049444449;T:1294288823;N:6107384 101 101     1290395271 1046629683 1049444449 1294288823 6107384 SRX8472318 SRS6772919 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.92236 0.92454 0.31359 0.31617 0.76625 0.76779 0.48273 0.47205 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59533 59533 SRR11926671 SRX8472317 SRS6772918 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   OPL3 GSM4591352   tissue:otg preleukemic thymocytes|cell type:thymocytes|genotype:otg;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab OPL3 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 otg preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:otg;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591352 GSM4591352: OPL3; Danio rerio; RNA Seq GSM4591352   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591352 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_35_R2.fastq.gz Fsample_35.fastq.gz fastq fastq 6253893538.0 30959869.0 GSM4591352 r1 0:101 1:101 A:1720308233;C:1397371474;G:1404797248;T:1723210472;N:8206111 101 101     1720308233 1397371474 1404797248 1723210472 8206111 SRX8472317 SRS6772918 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.93192 0.93318 0.35833 0.3632 0.78518 0.78788 0.48278 0.48009 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59534 59534 SRR11926670 SRX8472316 SRS6772917 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   OPL2 GSM4591351   tissue:otg preleukemic thymocytes|cell type:thymocytes|genotype:otg;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab OPL2 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 otg preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:otg;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591351 GSM4591351: OPL2; Danio rerio; RNA Seq GSM4591351   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591351 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_34_R2.fastq.gz Fsample_34.fastq.gz fastq fastq 5351903948.0 26494574.0 GSM4591351 r1 0:101 1:101 A:1442793834;C:1227325750;G:1233975738;T:1440891564;N:6917062 101 101     1442793834 1227325750 1233975738 1440891564 6917062 SRX8472316 SRS6772917 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.92964 0.93101 0.21706 0.2185 0.76497 0.76848 0.47634 0.48247 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59535 59535 SRR11926669 SRX8472315 SRS6772916 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   OPL1 GSM4591350   tissue:otg preleukemic thymocytes|cell type:thymocytes|genotype:otg;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab OPL1 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 otg preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:otg;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591350 GSM4591350: OPL1; Danio rerio; RNA Seq GSM4591350   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591350 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_33.fastq.gz Fsample_33_R2.fastq.gz fastq fastq 5499039536.0 27222968.0 GSM4591350 r1 0:101 1:101 A:1515036859;C:1226882670;G:1229198085;T:1520688016;N:7233906 101 101     1515036859 1226882670 1229198085 1520688016 7233906 SRX8472315 SRS6772916 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.92637 0.92762 0.31857 0.32243 0.76769 0.77116 0.46456 0.46584 101 101 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59546 59546 SRR11926658 SRX8472304 SRS6772905 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   MPL3 GSM4591339   tissue:hMYC preleukemic thymocytes|cell type:thymocytes|genotype:Tgrag2:hMYC Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab MPL3 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 hMYC preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tgrag2:hMYC Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591339 GSM4591339: MPL3; Danio rerio; RNA Seq GSM4591339   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591339 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_21.fastq.gz Fsample_21_R2.fastq.gz fastq fastq 8876009218.0 29390759.0 GSM4591339 r1 0:151 1:151 A:2397445782;C:2052027740;G:2018874313;T:2405562242;N:2099141 151 151     2397445782 2052027740 2018874313 2405562242 2099141 SRX8472304 SRS6772905 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.92414 0.9227 0.2461 0.23997 0.78841 0.79506 0.50203 0.5018 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59547 59547 SRR11926657 SRX8472303 SRS6772904 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   MPL2 GSM4591338   tissue:hMYC preleukemic thymocytes|cell type:thymocytes|genotype:Tgrag2:hMYC Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab MPL2 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 hMYC preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tgrag2:hMYC Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591338 GSM4591338: MPL2; Danio rerio; RNA Seq GSM4591338   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591338 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_20.fastq.gz Fsample_20_R2.fastq.gz fastq fastq 8942441970.0 29610735.0 GSM4591338 r1 0:151 1:151 A:2434196467;C:2047066969;G:2021293350;T:2437752994;N:2132190 151 151     2434196467 2047066969 2021293350 2437752994 2132190 SRX8472303 SRS6772904 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.9147 0.91499 0.22028 0.2117 0.77713 0.78334 0.50243 0.49838 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59548 59548 SRR11926656 SRX8472302 SRS6772903 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   MPL1 GSM4591337   tissue:hMYC preleukemic thymocytes|cell type:thymocytes|genotype:Tgrag2:hMYC Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab MPL1 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 hMYC preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:Tgrag2:hMYC Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591337 GSM4591337: MPL1; Danio rerio; RNA Seq GSM4591337   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591337 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_19.fastq.gz Fsample_19_R2.fastq.gz fastq fastq 9778540144.0 32379272.0 GSM4591337 r1 0:151 1:151 A:2676504038;C:2223347787;G:2177506547;T:2698864055;N:2317717 151 151     2676504038 2223347787 2177506547 2698864055 2317717 SRX8472302 SRS6772903 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.91346 0.91413 0.29555 0.28893 0.79078 0.79825 0.49875 0.50518 151 151 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59549 59549 SRR11926655 SRX8472301 SRS6772902 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   HPL3 GSM4591336   tissue:hulk mutant preleukemic thymocytes|cell type:thymocytes|genotype:hulk;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab HPL3 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 hulk mutant preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:hulk;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591336 GSM4591336: HPL3; Danio rerio; RNA Seq GSM4591336   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591336 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_12.fastq.gz Fsample_12_R2.fastq.gz fastq fastq 3378760800.0 16893804.0 GSM4591336 r1 0:100 1:100 A:869653801;C:820588210;G:823025653;T:861750769;N:3742367 100 100     869653801 820588210 823025653 861750769 3742367 SRX8472301 SRS6772902 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.93754 0.92151 0.17513 0.16969 0.79922 0.8071 0.63894 0.61913 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59550 59550 SRR11926654 SRX8472300 SRS6772901 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   HPL2 GSM4591335   tissue:hulk mutant preleukemic thymocytes|cell type:thymocytes|genotype:hulk;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab HPL2 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 hulk mutant preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:hulk;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591335 GSM4591335: HPL2; Danio rerio; RNA Seq GSM4591335   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591335 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_11.fastq.gz Fsample_11_R2.fastq.gz fastq fastq 3276290400.0 16381452.0 GSM4591335 r1 0:100 1:100 A:909076954;C:730010076;G:728583319;T:904911154;N:3708897 100 100     909076954 730010076 728583319 904911154 3708897 SRX8472300 SRS6772901 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.93409 0.92023 0.18134 0.18141 0.78108 0.78981 0.53659 0.52431 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
59551 59551 SRR11926653 SRX8472299 SRS6772900 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   HPL1 GSM4591334   tissue:hulk mutant preleukemic thymocytes|cell type:thymocytes|genotype:hulk;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab HPL1 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 hulk mutant preleukemic thymocytes   Truseq stranded mRNA library prep illumina #20020594   cell type:thymocytes|genotype:hulk;Tglck:GFP|tumor stg:preleukemic|lab of sample collection and sequencing:Frazer lab GSM4591334 GSM4591334: HPL1; Danio rerio; RNA Seq GSM4591334   1 Truseq stranded mRNA library prep illumina #20020594 GEO Accession:GSM4591334 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 3000   SRP265974     Fsample_10.fastq.gz Fsample_10_R2.fastq.gz fastq fastq 3700727800.0 18503639.0 GSM4591334 r1 0:100 1:100 A:1028412839;C:821049620;G:815741395;T:1031399520;N:4124426 100 100     1028412839 821049620 815741395 1031399520 4124426 SRX8472299 SRS6772900 SRA1083220 GEO Center for Medical Genetics, Ghent University 2 0.93381 0.92058 0.22321 0.22223 0.73655 0.74732 0.4822 0.48829 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Belgium 2020-06-04 Undetermined Undetermined Thymus Hematopoietic System
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
68889 68889 SRR18218067 SRX14364507 SRS12177802 SRP362416 PRJNA812715 Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia PRJNA812715 Other T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.         Thy rag2 RFP 6   strain:Tu/AB|age:not collected|sex:not collected|tissue:thymus|birth date: |death date:02 07 2019|genotype:rag2:RFP|biological replicate:Thy rag2 RFP biological replicate 4|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio thymus Tu/AB Thy rag2 RFP 6 Thy rag2 RFP 6 Tu/AB WT zebrafish were sacrificed to harvest the thymus visible through RFP staining for further analysis. The RNA was extracted from sorted thymic cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP362416     FCHT5GHDSXX_L1_HKRDZEBmfpEAAPRABPEI-P86H2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAPRABPEI-P86H2_2.fq.gz fastq fastq 18061636200.0 60205454.0 FCHT5GHDSXX L1 HKRDZEBmfpEAAPRABPEI P86H2 1.fq.gz 0:150 1:150 A:4749806271;C:4292116510;G:4365562558;T:4654124713;N:26148 150 150     4749806271 4292116510 4365562558 4654124713 26148 SRX14364507 SRS12177802 SRA1380603 Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab Instituto de Medicina Molecular Joao Lobo Antunes 2 0.9283 0.92884 0.11636 0.1154 0.77642 0.77697 0.48938 0.49117 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Portugal 2022-03-04 Undetermined Undetermined Thymus Hematopoietic System
68890 68890 SRR18218069 SRX14364506 SRS12177801 SRP362416 PRJNA812715 Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia PRJNA812715 Other T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.         Thy rag2 RFP 5   strain:Tu/AB|age:not collected|sex:not collected|tissue:thymus|birth date: |death date:02 07 2019|genotype:rag2:RFP|biological replicate:Thy rag2 RFP biological replicate 3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio thymus Tu/AB Thy rag2 RFP 5 Thy rag2 RFP 5 Tu/AB WT zebrafish were sacrificed to harvest the thymus visible through RFP staining for further analysis. The RNA was extracted from sorted thymic cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP362416     FCHT5GHDSXX_L1_HKRDZEBmfpEAAORAAPEI-P74G2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAORAAPEI-P74G2_2.fq.gz fastq fastq 16916167800.0 56387226.0 FCHT5GHDSXX L1 HKRDZEBmfpEAAORAAPEI P74G2 1.fq.gz 0:150 1:150 A:4469149097;C:4004191756;G:4070955203;T:4371847041;N:24703 150 150     4469149097 4004191756 4070955203 4371847041 24703 SRX14364506 SRS12177801 SRA1380603 Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab Instituto de Medicina Molecular Joao Lobo Antunes 2 0.92644 0.92786 0.13071 0.13011 0.77833 0.77792 0.47942 0.4816 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Portugal 2022-03-04 Undetermined Undetermined Thymus Hematopoietic System
68891 68891 SRR18218070 SRX14364505 SRS12177800 SRP362416 PRJNA812715 Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia PRJNA812715 Other T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.         Thy rag2 RFP 4   strain:Tu/AB|age:not collected|sex:not collected|tissue:thymus|birth date: |death date:02 07 2019|genotype:rag2:RFP|biological replicate:Thy rag2 RFP biological replicate 2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio thymus Tu/AB Thy rag2 RFP 4 Thy rag2 RFP 4 Tu/AB WT zebrafish were sacrificed to harvest the thymus visible through RFP staining for further analysis. The RNA was extracted from sorted thymic cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP362416     FCHT5GHDSXX_L1_HKRDZEBmfpEAANRABPEI-P62F2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAANRABPEI-P62F2_2.fq.gz fastq fastq 17996947500.0 59989825.0 FCHT5GHDSXX L1 HKRDZEBmfpEAANRABPEI P62F2 1.fq.gz 0:150 1:150 A:4882125302;C:4136332786;G:4194970590;T:4783492952;N:25870 150 150     4882125302 4136332786 4194970590 4783492952 25870 SRX14364505 SRS12177800 SRA1380603 Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab Instituto de Medicina Molecular Joao Lobo Antunes 2 0.86095 0.86165 0.25113 0.2504 0.80204 0.80188 0.48309 0.48627 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Portugal 2022-03-04 Undetermined Undetermined Thymus Hematopoietic System
68892 68892 SRR18218071 SRX14364504 SRS12177799 SRP362416 PRJNA812715 Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia PRJNA812715 Other T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.         Thy rag2 RFP 3   strain:Tu/AB|age:not collected|sex:not collected|tissue:thymus|birth date: |death date:02 07 2019|genotype:rag2:RFP|biological replicate:Thy rag2 RFP biological replicate 1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio thymus Tu/AB Thy rag2 RFP 3 Thy rag2 RFP 3 Tu/AB WT zebrafish were sacrificed to harvest the thymus visible through RFP staining for further analysis. The RNA was extracted from sorted thymic cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP362416     FCHT5GHDSXX_L1_HKRDZEBmfpEAAMRABPEI-P50E2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAMRABPEI-P50E2_2.fq.gz fastq fastq 18041602200.0 60138674.0 FCHT5GHDSXX L1 HKRDZEBmfpEAAMRABPEI P50E2 1.fq.gz 0:150 1:150 A:4726391295;C:4303349397;G:4380843440;T:4630991494;N:26574 150 150     4726391295 4303349397 4380843440 4630991494 26574 SRX14364504 SRS12177799 SRA1380603 Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab Instituto de Medicina Molecular Joao Lobo Antunes 2 0.93138 0.9316 0.11291 0.11196 0.78143 0.78261 0.4799 0.47958 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   Portugal 2022-03-04 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");;