|
| Status |
Public on Sep 20, 2020 |
| Title |
12-P2 |
| Sample type |
SRA |
| |
|
| Source name |
Rutgers/msh1
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Rutgers
genotype/variation: Rutgers/msh1
developmental stage: 6-week-old
tissue: young leaves
replicate type: biological rep 2
|
| Treatment protocol |
wedge grafting was carried out with seedlings at the two- to four-leaf stage following the procedure described in Yang et al, 2015
|
| Growth protocol |
Plants in the greenhouse were germinated on MetroMix 200 medium (SunGro) and maintained at 26-28°C with a 15-h day length and at 20-22.8°C with 9-h dark period.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ground tissue was processed with the DNeasy Plant Kit (Qiagen, Germany) for genomic DNA with RNA removal according to manufacturer protocol for subsequent bisulfite sequencing.
Genomic DNA was sonicated to 200-300bp by Covaris and the fragmented DNAs were tested by Gel-Electrophotometric and purified with MiniElute PCR Purification Kit (Qiagen, Germany), and incubated at 20 °C after adding End Repair Mix. DNA was purified, a single “A” nucleotide was added to the 3’ ends of blunt fragments, sample was re-purified and methylated adapter was added to 5’ and 3’ ends of each fragment. Fragments of 300–400bp were purified with QIAquick Gel Extraction Kit (Qiagen, Germany) and subjected to bisulfite treatment with the Methylation-Gold Kit (ZYMO), followed by PCR and gel purification (320–420bp fragments selected). Qualified libraries were paired-end sequenced on the Xten analyzer (150 bp read length
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.15 with cutoff 20
The sequences were aligned using Bismark (version 0.19.0) with default options.The deduplicate_bismark function in Bismark with default parameters was used to remove duplicated reads, and reads with coverage greater than 500 were removed to control PCR bias.
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: ITAG3.0
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>fields
|
| |
|
| Submission date |
Jun 16, 2020 |
| Last update date |
Sep 20, 2020 |
| Contact name |
Hardik Kundariya |
| E-mail(s) |
hsk13.psu@gmail.com
|
| Organization name |
The Pennsylvania State University
|
| Street address |
361 N. Frear
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16801 |
| Country |
USA |
| |
|
| Platform ID |
GPL25655 |
| Series (2) |
| GSE152568 |
Heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants [tomato_graft_methylome] |
| GSE152570 |
Heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants |
|
| Relations |
| BioSample |
SAMN15248579 |
| SRA |
SRX8554603 |
