run_metadata: 59577
This data as json
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| 59577 | SRR11926627 | SRX8472273 | SRS6772874 | 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 | PT1 2 | GSM4591308 | tissue:T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells.|cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab | PT1 2 | 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 | T ALL colleted when 90% of zebrafish was taken over by GFP + T ALL cells. | Truseq stranded mRNA library prep illumina #20020594 | cell type:T ALL|genotype:Tgrag2:hTLX1; rag2:GFP;phf6+/ |tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab | GSM4591308 | GSM4591308: PT1 2; Danio rerio; RNA Seq | GSM4591308 | 1 | Truseq stranded mRNA library prep illumina #20020594 | GEO Accession:GSM4591308 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP265974 | sample_8.fastq.gz | fastq | 2694796792.0 | 35662689.0 | GSM4591308 r1 | 0:75.56 1:0 | A:647242858;C:662131043;G:597596390;T:787640018;N:186483 | 75 | 0 | 647242858 | 662131043 | 597596390 | 787640018 | 186483 | SRX8472273 | SRS6772874 | SRA1083220 | GEO | Center for Medical Genetics, Ghent University | 1 | 0.94581 | 0.21549 | 0.79064 | 0.50568 | 76 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Belgium | 2020-06-04 | Undetermined | Undetermined | Cancer or Tumor | Cancer or Tumor |