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Series GSE229117 Query DataSets for GSE229117
Status Public on Dec 31, 2023
Title Priming of tomato mother plants using chemical elicitors linked to whole genome DNA methylation.
Organism Solanum lycopersicum
Experiment type Methylation profiling by high throughput sequencing
Summary Inbred parental lines of two cultivars (cv Moneyberg and cv Bolstar Granda) of the model crop tomato were primed (induced for resistance) during four different moments in their development, i.e. once in the vegetative phase (time window 1), once in the generative phase at early flowering (time window 2), multiple times in the generative phase during flowering (time window 3), and once during ripening of the first fruit bunch (time window 4). The primers were ß-aminobutyric acid (BABA), 2,6-dichloroisonicotinic acid (INA), methyljasmonate (MeJA), and water as control; they were selected for their ability to induce different plant resistance pathways. After collecting seed batches from these plants we here look at the effect of priming the tomato plants with those different chemicals on the plant genome methylation level.
 
Overall design Seeds from the same seed batch than the daughterplants displaying an improved resilience against pathogens were selected for DNA extraction : for Moneyberg, seeds from motherplants treated with BABA and Ina at time window 2 and treated with MeJa at time window 3, as well as seeds from control plants, for Bolstar: seeds from motherplants treated with BaBa and Ina at time window 2 as well as seeds from control plants.As a result, 48 seed samples were selected from the seed batches coming from 6 plants per treatments for the Bolstar cultivar and for the Moneyberg cultivar. 10 seeds per sample were pooled for each extraction. The extracted 48 DNA samples were sent to IGA technology to perform a whole genome bisulfite sequencing. A technical replicate was made for each sample resulting in 90 libraries. The libraries were prepared at the sequencing company. Sequencing was performed on a NovaSeq 6000 system generating 2*150bp paired end reads aiming for 10time coverage. Resulting sequences were obtained in fastq format.
 
Contributor(s) Duhamel M, van den Beld L
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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
Organization name Wageningen University & Research
Department Plant Science Group
Lab BioInteractions and Plant Health
Street address Droevendaalsesteeg 1
City Wageningen
ZIP/Postal code 6708PB
Country Netherlands
 
Platforms (1)
GPL27957 Illumina NovaSeq 6000 (Solanum lycopersicum)
Samples (96)
GSM7152820 seed, Moneyberg, Control, rep1; Chris1
GSM7152821 seed, Moneyberg, Control, rep2; Chris2
GSM7152822 seed, Moneyberg, Control, rep3; Chris3
Relations
BioProject PRJNA952987

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE229117_bb2.bed.gz 318.3 Kb (ftp)(http) BED
GSE229117_bi2.bed.gz 391.6 Kb (ftp)(http) BED
GSE229117_bw.bed.gz 350.7 Kb (ftp)(http) BED
GSE229117_mb2.bed.gz 405.0 Kb (ftp)(http) BED
GSE229117_mb3.bed.gz 405.0 Kb (ftp)(http) BED
GSE229117_mi2.bed.gz 406.5 Kb (ftp)(http) BED
GSE229117_mm3.bed.gz 391.7 Kb (ftp)(http) BED
GSE229117_mw.bed.gz 426.2 Kb (ftp)(http) BED
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