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Status |
Public on Jan 24, 2020 |
Title |
MiniCoopR-MyrRSK melanoma, rep4 |
Sample type |
SRA |
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Source name |
MiniCoopR-MyrRSK melanoma
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Organism |
Danio rerio |
Characteristics |
genotype: MiniCoopR-MyrRSK tissue: zebrafish melanoma
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Treatment protocol |
None
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Growth protocol |
Routine zebrafish husbandry
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
MC_MYR4
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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.
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Submission date |
Jan 23, 2020 |
Last update date |
Jan 25, 2020 |
Contact name |
Yariv Houvras |
Organization name |
Weill Cornell Medical College
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Department |
Surgery
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Street address |
1300 York Ave
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City |
New York |
State/province |
NY |
ZIP/Postal code |
10065 |
Country |
USA |
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Platform ID |
GPL14875 |
Series (1) |
GSE144117 |
Oxidative phosphorylation promotes primary melanoma invasion |
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Relations |
BioSample |
SAMN13908301 |
SRA |
SRX7622791 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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