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| Status |
Public on Jul 14, 2023 |
| Title |
Z141 Leaf tissue,DS |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Linum usitatissimum |
| Characteristics |
tissue: leaf
treatment: DS rep3
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted using CTAB method, the specific experimental steps are as described by Clarke(Clarke, 2009).
The Bisulfite-treated linseed DNA samples were used to prepare methylC-seq libraries. A total of 16 DNA samples (one control and three different drought treatments × two biological × two linseed varieties ) were sent to BioMarker Biotechnology Co., Ltd. (Beijing) for sequencing library construction and MethylC-sequencing. Sequencing libraries were prepared using a NEXTflex™ Bisulfite Sequencing Kit (PerkinElmer, USA) following the manufacturer’s recommendations, followed by MethylC-sequencing using the Illumina NovaSeq 6000 platform (San Diego, USA)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
remove the low quality reads and cut the adapters with fastp with default parameters
high-quality reads were mapped to the Lusitatissimum reference genome version (BGIv1.0) using BISMARK(v0.23.0)
The mapped reads were used to identify differentially methylated cytosines in each of 16 samples separately using the methylKit package
Cytosines were considered only if they were covered by at least 5 high-quality reads . Three methylation call files corresponding to the CG, CHG, and CHH sequence contexts were generated for each treatment
the Lusitatissimum genome was divided into 200-bp non-overlapping windows and used to identify differentially hyper- and hypomethylated regions (200-bp bins) in drought stress samples compared to the corresponding control samples using the methylKit package with a minimum methylation difference of 50% in the CG, 20% in the CHG and 10% in the CHH sequence contexts using a FDR of less than 5%.
Assembly: Lusitatissimum reference genome version (BGIv1.0)
Supplementary files format and content: each site methylation level in bedgraph format
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| Submission date |
Oct 19, 2022 |
| Last update date |
Jul 14, 2023 |
| Contact name |
Wei Wang |
| E-mail(s) |
ww9937@gmail.com
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| Organization name |
Chinese Academy of Agricultural Science
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| Department |
Ministry of Agriculture and Rural Affairs Oil Crops Research Institute
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| Lab |
Key Laboratory of Biology and Genetic Improvement of Oil Crops
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| Street address |
No.2 Xudong Road
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| City |
Wuhan |
| ZIP/Postal code |
430062 |
| Country |
China |
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| Platform ID |
GPL32467 |
| Series (1) |
| GSE213719 |
Alternative splicing and DNA methylation interact in linseed (Linum usitatissimum L.) response to different drought stresses |
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| Relations |
| BioSample |
SAMN31367393 |
| SRA |
SRX17956416 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6658484_Z141_DS_3.sorted.bedGraph.gz |
568.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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