{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"unknown\" and tissue_curation = \"Thymus\"", "rows": [[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. 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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. 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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. 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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. 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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", null, "pubmed:32591643", null, "OPL4", "GSM4591353", null, "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", null, "Truseq stranded mRNA library prep illumina  #20020594", null, "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", null, "1", "Truseq stranded mRNA library prep illumina  #20020594", "GEO Accession:GSM4591353", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP265974", null, null, "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, null, null, 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", null, "Belgium", "2020-06-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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", null, "pubmed:32591643", null, "OPL3", "GSM4591352", null, "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", null, "Truseq stranded mRNA library prep illumina  #20020594", null, "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", null, "1", "Truseq stranded mRNA library prep illumina  #20020594", "GEO Accession:GSM4591352", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP265974", null, null, "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, null, null, 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", null, "Belgium", "2020-06-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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", null, "pubmed:32591643", null, "OPL2", "GSM4591351", null, "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", null, "Truseq stranded mRNA library prep illumina  #20020594", null, "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", null, "1", "Truseq stranded mRNA library prep illumina  #20020594", "GEO Accession:GSM4591351", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP265974", null, null, "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, null, null, 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", null, "Belgium", "2020-06-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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", null, "pubmed:32591643", null, "OPL1", "GSM4591350", null, "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", null, "Truseq stranded mRNA library prep illumina  #20020594", null, "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", null, "1", "Truseq stranded mRNA library prep illumina  #20020594", "GEO Accession:GSM4591350", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP265974", null, null, "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, null, null, 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", null, "Belgium", "2020-06-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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", null, "pubmed:32591643", null, "MPL3", "GSM4591339", null, "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", null, "Truseq stranded mRNA library prep illumina  #20020594", null, "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", null, "1", "Truseq stranded mRNA library prep illumina  #20020594", "GEO Accession:GSM4591339", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP265974", null, null, "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, null, null, 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", null, "Belgium", "2020-06-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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", null, "pubmed:32591643", null, "MPL2", "GSM4591338", null, "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", null, "Truseq stranded mRNA library prep illumina  #20020594", null, "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", null, "1", "Truseq stranded mRNA library prep illumina  #20020594", "GEO Accession:GSM4591338", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP265974", null, null, "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, null, null, 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", null, "Belgium", "2020-06-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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", null, "pubmed:32591643", null, "MPL1", "GSM4591337", null, "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", null, "Truseq stranded mRNA library prep illumina  #20020594", null, "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", null, "1", "Truseq stranded mRNA library prep illumina  #20020594", "GEO Accession:GSM4591337", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP265974", null, null, "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, null, null, 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", null, "Belgium", "2020-06-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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", null, "pubmed:32591643", null, "HPL3", "GSM4591336", null, "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", null, "Truseq stranded mRNA library prep illumina  #20020594", null, "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", null, "1", "Truseq stranded mRNA library prep illumina  #20020594", "GEO Accession:GSM4591336", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP265974", null, null, "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, null, null, 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", null, "Belgium", "2020-06-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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", null, "pubmed:32591643", null, "HPL2", "GSM4591335", null, "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", null, "Truseq stranded mRNA library prep illumina  #20020594", null, "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", null, "1", "Truseq stranded mRNA library prep illumina  #20020594", "GEO Accession:GSM4591335", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP265974", null, null, "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, null, null, 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", null, "Belgium", "2020-06-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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", null, "pubmed:32591643", null, "HPL1", "GSM4591334", null, "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", null, "Truseq stranded mRNA library prep illumina  #20020594", null, "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", null, "1", "Truseq stranded mRNA library prep illumina  #20020594", "GEO Accession:GSM4591334", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP265974", null, null, "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, null, null, 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", null, "Belgium", "2020-06-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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.", null, null, null, null, "Thy rag2 RFP 6", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP362416", null, null, "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, null, null, 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", null, "Portugal", "2022-03-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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.", null, null, null, null, "Thy rag2 RFP 5", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP362416", null, null, "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, null, null, 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", null, "Portugal", "2022-03-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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.", null, null, null, null, "Thy rag2 RFP 4", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP362416", null, null, "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, null, null, 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", null, "Portugal", "2022-03-04", "Undetermined", "Undetermined", "Thymus", "Hematopoietic System"], [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.", null, null, null, null, "Thy rag2 RFP 3", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP362416", null, null, "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, null, null, 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, 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