run_metadata: 52101
This data as json
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| 52101 | SRR8928751 | SRX5709778 | SRS4648949 | SRP193005 | PRJNA533623 | MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease | GSE130037 | Transcriptome Analysis | The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma. | pubmed:31582381 | triple 3 | GSM3730544 | source name:Triple Superficial Melanoma|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K|tissue:Primary melanoma triple superficial | triple 3 | Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample | Triple Superficial Melanoma | Whole tumour was dissected dissociated and RNA extracted using Trizol with column cleanup polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads | genotype:mitfa:BRAFV600E;mitfavc7;p53M214K|tissue:Primary melanoma triple superficial | GSM3730544 | GSM3730544: triple 3; Danio rerio; RNA Seq | GSM3730544 | 1 | Whole tumour was dissected dissociated and RNA extracted using Trizol with column cleanup polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads | GEO Accession:GSM3730544 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP193005 | JT-Triple-3_S3_L003_R1_001.fastq.gz JT-Triple-3_S3_L003_R2_001.fastq.gz | fastq fastq | 1947408108.0 | 12897369.0 | GSM3730544 r3 | 0:75.54 1:75.46 | A:496173657;C:475558325;G:471420009;T:504165219;N:90898 | 75 | 75 | 496173657 | 475558325 | 471420009 | 504165219 | 90898 | SRX5709778 | SRS4648949 | SRA876955 | GEO | Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC | 2 | 0.94968 | 0.95322 | 0.057 | 0.05543 | 0.69731 | 0.69877 | 0.50204 | 0.5021 | 76 | 76 | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | nextera | bulk | bulk | bulk | United Kingdom | 2019-04-18 | Undetermined | Undetermined | Cancer or Tumor | Cancer or Tumor |