RNA-Seq of Carcharodon carcharias of epidermis sample - SRA

SRX4627241: RNA-Seq of Carcharodon carcharias of epidermis sample
1 ILLUMINA (Illumina HiSeq 4000) run: 101M spots, 30.5G bases, 12.4Gb downloads

Design: RNA was isolated from sample using the Zymo Research Direct-zol kit. Total RNA was examined for RNA Integrity Numbers and all samples had values >7. To generate paired-end mRNA sequencing libraries, we used the Illumina mRNA TruSeq kit, which included a poly-A selection module, and sequenced libraries on an Illumina 4000 at the Stanford University Functional Genomics Facility. All raw read files were trimmed and process for paired reads only using default parameters for Trimmomatic v0.36.

Submitted by: California State University, Monterey Bay

Study: Carcharodon carcharias Transcriptome or Gene expression

PRJNA485795 • SRP159201 • All experiments • All runs

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White shark transcriptome assembly from RNA isolated from 3 individuals and 5 different tissues (heart tissue from the previous BioProject: PRJNA177971, muscle, subdermis, epidermis, and blood). This de novo assembled transcriptome was used for annotation of white shark genome assembly. RNA-seq reads from new tissues (i.e. not heart) were assembled into transcriptomes using Trinity, TransAbyss, and Oases and then collapsed, along with a previously assembly heart transcriptome, into 1 final transcriptome assembly using the EviGene pipeline

Sample: Tissue plug sample from Carcharodon carcharias male

SAMN09814228 • SRS3728702 • All experiments • All runs

Organism: Carcharodon carcharias

Library:

Name: Epidermis-GCCAAT_S2

Instrument: Illumina HiSeq 4000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: other

Layout: PAIRED

Runs: 1 run, 101M spots, 30.5G bases, 12.4Gb

Run	# of Spots	# of Bases	Size	Published
SRR7771834	100,973,803	30.5G	12.4Gb	2019-09-30

ID:: 6251314

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