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Sample GSM4074980

Query DataSets for GSM4074980

Status

Public on Sep 13, 2019

Title

Leaf, STV-free, rep2

Sample type

SRA

Source name

leaf

Organism

Solanum lycopersicum

Characteristics

cultivar: M82
age: 1-month-old
virus infection: STV-free
tissue: leaf

Extracted molecule

total RNA

Extraction protocol

Total RNAs were extracted by using the Trizol reagent following the manufacturer’s protocol (Thermo Fisher Scientific, Japan).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

Sample 432

Data processing

Illumina Casava ver.1.8.2 software was used for base calling.
Sequenced reads were mapped to the tomato genome (Tomato SL2.50 ITAG2.4; Sol Genomic Network https://solgenomics.net/) using TopHat ver. 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19 (Trapnell et al., 2009).
The number of fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm ver. 2.2.1 (Trapnell et al., 2010).
Genome_build: Tomato SL2.50 ITAG2.4; Sol Genomic Network https://solgenomics.net/
Supplementary_files_format_and_content: FPKM, Processed Signal, count

Submission date

Sep 12, 2019

Last update date

Sep 13, 2019

Contact name

Midori Tabara

E-mail(s)

mtabara@fc.ritsumei.ac.jp

Organization name

Ritsumeikan University

Street address

1-1-1, Noji-Higashi