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Sample GSM4280507 Query DataSets for GSM4280507
Status Public on Jan 24, 2020
Title MiniCoopR-GFP melanoma, rep1
Sample type SRA
 
Source name MiniCoopR-GFP melanoma
Organism Danio rerio
Characteristics genotype: MiniCoopR-GFP
tissue: zebrafish melanoma
Treatment protocol None
Growth protocol Routine zebrafish husbandry
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated using Rneasy plus mini kit (Qiagen) according to the manufacturer's protocol
Library construction was performed using Illumina reagents according to the manufacturer's protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description MC_GFP1
Data processing Reads were aligned using STAR (v2.6.1d), Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR: STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England) 2013, 29:15-21.
Read counting was performed using htseq-count v0.6.0
Differential gene expression was performed using Deseq2, Love MI, Huber W, Anders S: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology 2014, 15:550.
Genome_build: Zv9
Supplementary_files_format_and_content: Differential gene expression was performed using Deseq2 and outputted in a .csv file with ensembl gene identifiers.
 
Submission date Jan 23, 2020
Last update date Jan 25, 2020
Contact name Yariv Houvras
Organization name Weill Cornell Medical College
Department Surgery
Street address 1300 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL14875
Series (1)
GSE144117 Oxidative phosphorylation promotes primary melanoma invasion
Relations
BioSample SAMN13908281
SRA SRX7622782

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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