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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2023 |
| Title |
sldml2_season2_1 |
| Sample type |
SRA |
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| Source name |
Fruits
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| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: fruit
cultivar: Ailsa Craig (AC)
genotype: sldml2
season: season2
replicate: 1
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| Growth protocol |
Wild type tomato (Solanum lycopersicum) Ailsa Craig (AC), NAC-NOR CRISPR mutant (slnor), and SlDML2 CRIPSR mutant (sldml2) plants (AC background) were grown in a condition-controlled greenhouse (16 h:8 h, 25 ℃:20 ℃, light:dark cycle).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
WGBS was performed according to a previous published protocol (Zhang et al., 2016).
DNA samples were sent to LC-Bio Technologies (Hangzhou) CO., LTD. (Hangzhou, China) for library construction and sequencing or sent to the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for library construction and Illumina sequencing.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
To remove low-quality sequence and adapters via Trimmomatic (Bolger, Lohse, & Usadel, 2014) was used
The paired-end reads were mapped to the SL4.0 genome of Solanum lycopersicum by BSMAP with -r parameter to remove PCR duplications
To extract methylation ratio with methyratio.py script from BASMAP
DMRs and DMCs were identified using the R packages, methylKit (Akalin et al., 2012)
Genome_build: SL4.0
Supplementary_files_format_and_content: Bigwig files that represent the number of reads that contain methylated sites
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| Submission date |
Jan 06, 2022 |
| Last update date |
Dec 31, 2023 |
| Contact name |
yujing lin |
| E-mail(s) |
linyj3@sustech.edu.cn
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| Phone |
+8618259081781
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| Organization name |
Southern University of Science and Technology
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| Street address |
No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen City, Guangdong Province
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| City |
Shenzhen |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platform ID |
GPL25655 |
| Series (1) |
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| Relations |
| BioSample |
SAMN24694918 |
| SRA |
SRX13640118 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5775820_sldml2_season2_1_mC.bw |
462.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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