run_metadata: 41566
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41566 | SRR5044689 | SRX2367698 | SRS1813796 | SRP093723 | PRJNA354577 | RNA seq of zebrafish melanoma cells post metastatic dissemination | GSE90143 | Transcriptome Analysis | We report how the zebrafish melanoma cell line ZMEL1 changes post intravascular injection into 2dpf zebrafish embryos as compared to the cells growing in vitro. Overall design: Examination of ZMEL1 cells in vitro versus 21 days in vivo in the zebrafish | pubmed:28181494 | ZMEL1 METASTATIC REP 3 | GSM2399712 | tissue:ZMEL1 cells in vivo|cell type:ZMEL1|tissue type:melanoma | ZMEL1 METASTATIC REP 3 | GSNAP alignment to Av9 zebrafish reference genome Read counts extracted with HTSeq Differential expression with DeSeq2 Zebrafish genes converted to human orthologs using DIOPT Genome build: Zv9 Supplementary files format and content: XLSX sheet with normalized read counts output from HTSeq | ZMEL1 cells in vivo | n/a | Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq | in vitro: DMEM/10% FCS/1X glutamax/28.5C in vivo: growth in the zebrafish from 2 21dpf | cell type:ZMEL1|tissue type:melanoma | GSM2399712 | GSM2399712: ZMEL1 METASTATIC REP 3; Danio rerio; RNA Seq | GSM2399712 | 1 | Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq | GEO Accession:GSM2399712 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP093723 | DISSEMINATED-4-GFP-POS_AGTTCC_AHBENJADXX_L001_001.R1.fastq | fastq | 547347950.0 | 10946959.0 | GSM2399712 r1 | 0:50 | A:142532772;C:118021475;G:130457816;T:156280877;N:55010 | 50 | 142532772 | 118021475 | 130457816 | 156280877 | 55010 | SRX2367698 | SRS1813796 | SRA497524 | GEO | White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center | 1 | 0.82238 | 0.37848 | 0.81511 | 0.68704 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2016-11-22 | Larval | Larval | Cancer or Tumor | Cancer or Tumor |