|
| Status |
Public on Jun 22, 2021 |
| Title |
WT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Ailsa Craig
|
| Organism |
Solanum lycopersicum |
| Characteristics |
time point: At 38 days after anthesis (dpa)
tissue: Pericarp
genotype/variation: WT
|
| Growth protocol |
Wild-type tomato and transgenic lines in the Ailsa-Craig background were grown in a greenhouse at 23°C under 16 h light and 8 h dark condition.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5 g tomato sample were used to extract DNA. The qualified DNA was fragmented with an ultrasonic disruptor (Bioruptor), with an average size of about 300-500 bp.
Fragmented DNA were end-repaired and ligated to a fully methylated adapter by using NEXTflex™ Bisulfite-Seq Barcodes-6 Kit (51191, Bioo Scientific). Using EZ DNA Methylation-Gold ™ kit (Zymo Research Corp., catalog number D5005) for bisulfite conversion of adapter-linked DNA. After amplification by PCR, the high-quality library has a DNA fragment distribution of about 300 bp
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina PE150 software used for sequencing analysis
Filtered out low quality data, only clean data were used for the further methylation related statistics. The clean reads were then mapped to reference genome by the BSseeker software. CGmap Tools software were used to count the depth of sequencing of C bases across the genome.
Methylation level was determined by dividing the number of reads covering each mC by the total number of reads covering that cytosine, which was also equal to the mC/C ratio at each reference cytosine.
CGmap Tools was used to count the average of C-base methylation levels in various types. Recalculate the distribution ratio of methylation C sites (mC) in different types. Based on the methGO software, we give the copy number change of each sample gene
We used the circlize package to plot the distribution of methylated C sites, DMR and CNV on the genome[6], CGmap Tools software (version: 0.1.1) also was used to map the methylation level distribution of the gene region and the 2 kb region upstream and downstream for all sample.The motif feature sequences corresponding to all DMR regions are passed through Homer software (version 3) predict motif
Genome_build: Tomato reference genome (version SL3.0)
|
| |
|
| Submission date |
Jun 23, 2020 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Ding xiaochun |
| E-mail(s) |
dingxc111@scbg.ac.cn
|
| Organization name |
SOUTH CHINA BOTANICAL GARDEN
|
| Street address |
723 xingke road, tianhe district
|
| City |
guangzhou city |
| State/province |
guangdong |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL25655 |
| Series (1) |
| GSE153080 |
Histone demethylase SlJMJ7 Integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato |
|
| Relations |
| BioSample |
SAMN15352099 |
| SRA |
SRX8603223 |
