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Sample GSM5929310

Query DataSets for GSM5929310

Status

Public on Mar 05, 2022

Title

leaf, Zn_CMV_3

Sample type

SRA

Source name

leaf

Organism

Arabidopsis halleri

Characteristics

tissue: leaf
cultivar: 4K
infection: cucumber mosaic virus (CMV), Zn

Extracted molecule

total RNA

Extraction protocol

Total RNAs were extracted by using the Trizol reagent following the manufacturer’s protocol (Thermo Fisher Scientific, MA).
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

Data processing

Illumina Casava ver.1.8.2 software was used for base calling.
Sequenced reads were mapped to the A. halleri genome (Briskine et al., 2017) using TopHat (ver. 2.0.13) in combination with Bowtie2 (ver. 2.2.3) (Langmead & Salzberg, 2012) and SAMtools (ver. 0.1.19).
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).
We obtained the annotation data from Ensemblgenome (https://plants.ensembl.org/Arabidopsis_halleri/Info/Index).
Genome_build: A. halleri genome (Briskine et al., 2017)
Supplementary_files_format_and_content: counts

Submission date

Mar 02, 2022

Last update date

Mar 05, 2022

Contact name

Midori Tabara

E-mail(s)

mtabara@fc.ritsumei.ac.jp

Organization name

Ritsumeikan University

Street address

1-1-1, Noji-Higashi