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| Status |
Public on Apr 04, 2022 |
| Title |
CTR1 |
| Sample type |
SRA |
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| Source name |
mock-treated leaves
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| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Money Maker
tissue: leaves
age: 21 days
treatment: mock
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| Treatment protocol |
Seven-day-old seedlings were root-drenched with a volume of 5 mM BABA equivalent to one tenth of the volume of the compost growing medium to achieve a final concentration of 0.5 mM BABA around the root system. Control plants were mock-treated with a water root drench. One week later, seedlings were removed from the compost, their root systems rinsed in water and then re-potted to new compost.
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| Growth protocol |
Tomato seedlings germinated in a peat-based compost mixture grown in a heated, passively ventilated glasshouse (min 18 °C max 25 °C), with supplementary lighting (minimum 250±25 μmol m-2s-1 PAR, for 16-hours photoperiod).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Qiagen Plant DNeasy kit (Qiagen).
Libraries were constructed starting from genomic DNA and sequenced by GATC Biotech AG (Konstanz, Germany)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Whole genome bisulfite sequencing (WGBS) datasets (fastq files) were trimmed using Trimmomatic (Bolger et al., 2014) to remove adapter sequences
High-quality trimmed sequences were aligned against the tomato reference genome using Bismark (Krueger & Andrews, 2011). Duplicated reads were collapsed into one read.
Chloroplast sequences (NC_007898.3) was used to estimate the bisulfite conversion.
To account for non-converted DNA, we applied a correction according to Catoni and Zabet 2021 (https://doi.org/10.1007/978-1-0716-1134-0_21). Briefly, the number of methylated reads were decreased as: m*= max(0, m – nc) (where m* is the corrected number of methylated reads, m is the raw number of methylated reads, n is the total number of reads and c is the conversion rate).
Genome_build: SL3.0
Supplementary_files_format_and_content: For each genotype, the CX_Report generated by Bismark is provided (Krueger et al. 2011, Bioinformatics), after correction for non-converted DNA has been applied.
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| Submission date |
Dec 13, 2021 |
| Last update date |
Apr 04, 2022 |
| Contact name |
Marco Catoni |
| Organization name |
University of Birmingham
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| Department |
School of Biosciences
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| Street address |
Edgbaston
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| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
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| Platform ID |
GPL19694 |
| Series (2) |
| GSE190780 |
Long-lasting priming by β-amino butyric acid is marked by DNA hypomethylation |
| GSE190782 |
Long-lasting priming by β-amino butyric acid is marked by DNA hypomethylation. |
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| Relations |
| BioSample |
SAMN23998101 |
| SRA |
SRX13395799 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5731683_CTR1_corrected.CX_report.txt.gz |
992.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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