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Status |
Public on Dec 31, 2023 |
Title |
seed, Bolstar, BABA_TW2, rep4; Chrisbis34 |
Sample type |
SRA |
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Source name |
seed
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Organism |
Solanum lycopersicum |
Characteristics |
tissue: seed genotype: Bolstar treatment: BABA_TW2
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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).
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
bb2.bed
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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.
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Submission date |
Apr 06, 2023 |
Last update date |
Dec 31, 2023 |
Contact name |
Marie Duhamel |
E-mail(s) |
marie.duhamel@wur.nl
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Organization name |
Wageningen University & Research
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Department |
Plant Science Group
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Lab |
BioInteractions and Plant Health
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Street address |
Droevendaalsesteeg 1
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City |
Wageningen |
ZIP/Postal code |
6708PB |
Country |
Netherlands |
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Platform ID |
GPL27957 |
Series (1) |
GSE229117 |
Priming of tomato mother plants using chemical elicitors linked to whole genome DNA methylation. |
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Relations |
SRA |
SRX19897784 |
BioSample |
SAMN34100715 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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