run_metadata: 41570
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 41570 | SRR5044686 | SRX2367696 | SRS1813795 | 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 1 | GSM2399710 | tissue:ZMEL1 cells in vivo|cell type:ZMEL1|tissue type:melanoma | ZMEL1 METASTATIC REP 1 | 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 | GSM2399710 | GSM2399710: ZMEL1 METASTATIC REP 1; Danio rerio; RNA Seq | GSM2399710 | 1 | Cells were FACS sorted and total RNA isolated with Zymo kits Illumina TruSeq | GEO Accession:GSM2399710 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP093723 | DISSEMINATED-1-GFP-POS_GGCTAC_AC62F2ANXX_L006_001.R1.fastq DISSEMINATED-1-GFP-POS_GGCTAC_AC62F2ANXX_L006_001.R2.fastq | fastq fastq | 1056705000.0 | 10567050.0 | GSM2399710 r1 | 0:50 1:50 | A:276214070;C:230055594;G:254656322;T:295743831;N:35183 | 50 | 50 | 276214070 | 230055594 | 254656322 | 295743831 | 35183 | SRX2367696 | SRS1813795 | SRA497524 | GEO | White Lab, Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center | 2 | 0.87206 | 0.87707 | 0.36 | 0.36551 | 0.80661 | 0.81442 | 0.67855 | 0.54025 | 50 | 50 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2016-11-22 | Larval | Larval | Cancer or Tumor | Cancer or Tumor |