run_metadata: 59565
This data as json
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| 59565 | SRR11926639 | SRX8472285 | SRS6772885 | 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 | T2 1 | GSM4591320 | 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|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab | T2 1 | 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|tumor stg:Transplant T ALL|lab of sample collection and sequencing:Speleman lab | GSM4591320 | GSM4591320: T2 1; Danio rerio; RNA Seq | GSM4591320 | 1 | Truseq stranded mRNA library prep illumina #20020594 | GEO Accession:GSM4591320 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP265974 | sample_20.fastq.gz | fastq | 3407895222.0 | 45108733.0 | GSM4591320 r1 | 0:75.55 1:0 | A:772284922;C:869002714;G:804588273;T:961751439;N:267874 | 75 | 0 | 772284922 | 869002714 | 804588273 | 961751439 | 267874 | SRX8472285 | SRS6772885 | SRA1083220 | GEO | Center for Medical Genetics, Ghent University | 1 | 0.96729 | 0.10404 | 0.80819 | 0.50282 | 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 |