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Sample GSM7118445

Query DataSets for GSM7118445

Status

Public on Sep 01, 2023

Title

Tolerant callus line L3, exposed to fungal filtrate TCLF3

Sample type

SRA

Source name

Callus

Organism

Persea americana

Characteristics

cultivar: Anaheim
tissue: Callus
cell line: L3
phenotype: Tolerant
cell type: Embryogenic
treatment: Exposed to fungal filtrate

Treatment protocol

The virulent CH53 fungal strain of Rosellinia necatrix was cultured on potato dextrose agar (PDA) in darkness at 25 °C. To obtain the fungal filtrate, six 1cm-fragments of PDA with fungal mycelium were incubated on 500ml of PDA liquid medium during 9 days at 25 °C in darkness. This medium was filtrated through 2 layers paper to eliminate hyphae and remains of the fungus; the medium obtained was sterilized through 0.2 µm filtration and frozen until its use.

Growth protocol

The embryogenic cultures were maintained on Murashige and Skoog (MS) medium (Murashige & Skoog, 1962) supplemented with 0.1 mg l-1 picloram (MSP medium) and solidified with 6 g l-1 agar in darkness at 25 ± 1 °C and were subculture at 4-week intervals in MSP medium. The pH medium was adjusted to 5.74 before to autoclaving at 0.1 MPa and 121 °C for 15 min.

Extracted molecule

total RNA

Extraction protocol

For RNA extraction, the embryogenic callus from L3 and AN9 exposed and no exposed to fungal exudates were macerated with liquid nitrogen. And, afterwards, RNA was extracted using ´Spectrum plant RNA kit´ (Sigma Aldrich) following manufacturer’s instructions.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

R12TCLF

Data processing

Raw data in a FASTQ format were processed using fastp.
Raw reads were processed to remove reads containing adapter and poly-N sequences and reads with low quality and were calculated the Q20, Q30 and GC content of the clean data (clean reads).
High quality paired-end clean reads were mapped to the reference genome downloaded from genome website browser (NCBI) using HISAT2 software.
Differential expression analysis of three biological replicates per condition was performed using DESeq2 R package. Benjamin and Hochberg’s approach were used to adjust P values for controlling the False Discovery Rate (FDR) and select genes with an adjusted Pvalue < 0.05 as differentially expressed genes.
The main purpose of this study is to compare and analyse differential expressed genes (DEGs) and differential pathways after growing two different avocado lines (S, Susceptible and T, Tolerant) on media supplemented with Rosellinia necatrix filtrates.
A differential expression analysis is made. The input data for differential gene expression analysis is read counts from gene expression level analysis. The differential gene expression analysis contains three steps: read counts normalization; model dependent p-value estimation; FDR value estimation based on multiple hypothesis testing.
Assembly: not provided
Supplementary files format and content: Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.

Submission date

Mar 27, 2023

Last update date

Sep 01, 2023

Contact name

Clara Pliego

E-mail(s)

mclara.pliego@juntadeandalucia.es

Phone

0034654564365

Organization name

IFAPA