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Sample GSM5905623

Query DataSets for GSM5905623

Status

Public on Feb 20, 2022

Title

Infected with Lso haplotype B, rep 3 [J3-3_S57]

Sample type

SRA

Source name

leaf tissue

Organism

Solanum lycopersicum

Characteristics

tissue: leaf
variety: Moneymaker
age: 9 weeks
treatment: Infected with Lso haplotype B

Extracted molecule

total RNA

Extraction protocol

Plant RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

cDNA libraries were developed using the TruSeq RNA Library Prep Kit v2 following the manufacturer's protocol
Libraries were multiplexed and sequenced on the Illumina PE HiSeq 2500 v4 platform
Sequence cluster identification, quality prefiltering, base calling, and uncertainty assessment were done in real time using Illumina’s HCS 2.2.38 and RTA 1.18.61 software with default parameter settings
bioinformatic analysis was performed using the HISAT2-StringTie-Ballgown RNA-Seq workflow
Genome_build: Libraries reads were mapped to the S. lycopersicum genome (vSL3.0) using HISAT2; StringTie assembled hits to known transcripts based on the vITAG3.2 annotation
Supplementary_files_format_and_content: Matrix table with fpkm (Fragments Per Kilobase of transcript per Million mapped reads) values for every gene and every sample

Submission date

Feb 17, 2022

Last update date

May 10, 2022

Contact name

Kyle Harrison

E-mail(s)

kyle.harrison@usda.gov

Organization name

Texas A&M University

Department

Entomology