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Sample GSM3855538

Query DataSets for GSM3855538

Status

Public on Jul 04, 2019

Title

Graft sp//SFT-rep2

Sample type

SRA

Source name

stem

Organism

Solanum lycopersicum

Characteristics

experiment: Graft
genotype/variation: 35S:SFT//sp

Extracted molecule

total RNA

Extraction protocol

Five, seemingly homogeneous plants were selected from a larger population to represent the natural variation among greenhouse tomato plants. Independent stem samples consisted of 5 mid-segments of internodes harvested in duplicates 2 h after dawn. Total RNA was extracted using the RNeasy Mini Kit (Qiagen), and treated with DNase I using the RNase-Free DNase set (Qiagen)
RNA samples were processed for sequencing, quality control, and differential expression analysis at the Technion Genome Center. Libraries of single 50 bp reads were prepared using the Ilumina TruSeq RNA library preparation kit v2. The barcoded libraries were sequenced on Ilumina Hiseq 2500, six samples per lane (~30,000,000 reads). If an experiment included more than 6 samples, each sample was divided equally, in all the lanes.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

Sample_289

Data processing

Library quality control was conducted using FASTQC, version 0.11.5
Sequences were trimmed by quality using trim galore
Sequences were aligned using Tophat2, version 2.1.0 (uses Bowtie2 version 2.2.6).
Raw gene expression levels were counted by HTseq-count, version 0.6.1
Genome_build: ITAG version 2.5 genome (ftp://ftp.sgn.cornell.edu/genomes/Solanum_lycopersicum/annotation/ITAG2.5_release),
Supplementary_files_format_and_content: counts

Submission date

Jun 06, 2019

Last update date

Jul 04, 2019

Contact name

Eliezer Lifschitz

Organization name

Technion

Department

Faculty of Biology

Street address

Technion City