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Sample GSM7152899

Query DataSets for GSM7152899

Status

Public on Dec 31, 2023

Title

seed, Bolstar, BABA_TW2, rep2; Chrisbis32

Sample type

SRA

Source name

seed

Organism

Solanum lycopersicum

Characteristics

tissue: seed
genotype: Bolstar
treatment: BABA_TW2

Extracted molecule

genomic DNA

Extraction protocol

The DNA extraction was performed following the manufacturer instructions using the Quick-DNA Plant/Seed Miniprep Kit from Zymoresearch. For each sample the DNA concentration and quality was measured using a Qubit fluorometer.
Ultralow Methyl-Seq System (Tecan/NuGEN, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions. DNA samples were quantified with Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay (Agilent technologies, Santa Clara, CA).
Libraries were then prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeq6000 (Illumina, San Diego, CA).

Library strategy

Bisulfite-Seq

Library source

genomic

Library selection

RANDOM

Instrument model

Illumina NovaSeq 6000

Description

bb2.bed

Data processing

To analyse the raw sequences obtained and estimate methylation levels per chromosome and compare them across treatment between controls and seeds from plants primed by Ina, BaBa and MeJa, we used the pipeline MethPipe (Song et al.,2013)
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for adapter trimming as well as quality control, with some added functionality to remove biased methylation positions.
Abismal (de Sena Brandine et al., 2021) was used to construct the methylome and map bisulfite treated short reads on the tomato plant genome.
Supplementary files format and content: The file mw.bed is in a bed format and contains information of the hypomethylated regions from the genome of control Moneyberg tomato seeds (from untreated plants).
Supplementary files format and content: The file mb2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with Baba in time window 2.
Supplementary files format and content: The file mi2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with Ina in time window 2.
Supplementary files format and content: The file mm3.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with MeJA in time window 3.
Supplementary files format and content: The file mb3.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Moneyberg tomato seeds from plants treated with MeJA in time window 3.
Supplementary files format and content: The file bb2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Bolstar tomato seeds from plants treated with Baba in time window 2.
Supplementary files format and content: The file bw.bed is in a bed format and contains information of the hypomethylated regions from the genome of the control Bolstar tomato seeds (from untreated plants).
Supplementary files format and content: The file bi2.bed is in a bed format and contains information of the hypomethylated regions from the genome of the Bolstar tomato seeds from plants treated with Ina in time window 2.

Submission date

Apr 06, 2023

Last update date

Dec 31, 2023

Contact name

Marie Duhamel

E-mail(s)

marie.duhamel@wur.nl

Organization name

Wageningen University & Research

Department

Plant Science Group