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Sample GSM4176233

Query DataSets for GSM4176233

Status

Public on May 07, 2020

Title

RNAseq from leaf tissue, biological replicate 1

Sample type

SRA

Source name

Whole leaf

Organism

Olea europaea

Characteristics

developmental stage: Adult
cultivar: Picual
tissue: Whole leaf

Extracted molecule

total RNA

Extraction protocol

Spectrum Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO) used according to the manufacturer’s instructions
A pool of the cDNA libraries was sequenced by paired-end sequencing (101 x 2) with an Illumina HiSeq 2000 sequencer. Two biological replicates per sample were sequenced, and each replicate was loaded twice on two different lanes in the flow cell.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

PolyA RNAseq

Data processing

Raw Illumina RNAseq reads were first preprocessed using Fastqmcf by discarding primers and reads with adaptors, unknown nucleotides, and poor-quality or short-length reads, increasing the Q score to more than 30 for all the libraries and filtering for lengths greater than 50 bp (Q30L50)
Quality control of sequencing was performed using NGS_QC software
Trimming and cleaning of the obtained reads was performed using the software Trimgalore
The gene-expression study was made with the DNAStar (ArrayStar 15) Qseq software for RNAseq analysis (www.dnastar.com). Reads were mapped to Olea europaea cv. Picual genome as the reference Oleur061. We undertook mapping using parameters k-mer = 63 and 95% of matches and used the default normalization method of ‘reads per kilobase per million mapped reads’, RPKM. The number of replicates per sample for expression average calculation was two. A basal expression level of log2 RPKM = -2 was considered, so only genes with expression values above this threshold level were considered as expressed, and those with values equal or below the threshold level were considered as not expressed.
Genome_build: Oleur061 assembled genome from Olea europaea cv. Picual (PRJNA556567)
Supplementary_files_format_and_content: Matrix table with gene’s IDs and their linear RPKM counts

Submission date

Nov 19, 2019

Last update date

May 07, 2020

Contact name

Jorge Antolín Ramirez

E-mail(s)

jrtejero@ujaen.es

Phone

671120212

Organization name

University of Jaen