run_metadata: 41569
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41569 | SRR5044688 | SRX2367697 | SRS1813798 | 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 2 | GSM2399711 | tissue:ZMEL1 cells in vivo|cell type:ZMEL1|tissue type:melanoma | ZMEL1 METASTATIC REP 2 | 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 | GSM2399711 | GSM2399711: ZMEL1 METASTATIC REP 2; Danio rerio; RNA Seq | GSM2399711 | 1 | Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq | GEO Accession:GSM2399711 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP093723 | DISSEMINATED-3-GFP-POS_AGTCAA_AHBENJADXX_L002_001.R1.fastq | fastq | 452003900.0 | 9040078.0 | GSM2399711 r2 | 0:50 | A:119365829;C:96270497;G:105927958;T:129699772;N:739844 | 50 | 119365829 | 96270497 | 105927958 | 129699772 | 739844 | SRX2367697 | SRS1813798 | SRA497524 | GEO | White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center | 1 | 0.8334 | 0.39284 | 0.78033 | 0.63687 | 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 |