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| Status |
Public on Feb 07, 2019 |
| Title |
WGBS_fwa_FigureS1 |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaf
genotype: fwa
ecotype: Columbia
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| Growth protocol |
All plants in this study were grown under long-day conditions (16h light/8h dark). Transgenic plants were obtained by agrobacterium-mediated floral dipping. T1 transgenic plants were selected on 1/2 MS medium + Glufosinate 50 μg/ml (Goldbio) or 1/2 MS medium + Hygromycin B 25 μg/ml (Invitrogen) in growth chambers under long day conditions and subsequently transferred to soil. Successive transgenic generations were germinated directly on soil.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries for WGBS were made using 100ng of CTAB-extracted DNA from leaves of adult plants.
DNA was converted using the Epitect Bisulfite Conversion kit (Qiagen) and libraries were prepared using the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
WGBS for fwa used for FigureS1
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| Data processing |
For WGBS data analysis, raw reads were aligned using with BSMAP (v 2.74) (Xi and Li, 2009) to the reference TAIR10 genome by allowing up to 2 mismatches (-v 2), 1 best hit (-w 1) and aligning to both strands(-n 1). Methylation levels at each cytosine were then extracted with BSMAP (methratio.py) scripts by allowing only unique mapped reads (-u). Reads with more than 3 consecutive methylated CHH sites were removed. Methylation levels at each cytosine were calculated as #C/(#C+#T). DMRs between DMS3-ZF and ZF, NRPD1-ZF and ZF, DMS3-ZF X NRPD1-ZF and ZF were calculated as before (Stroud et al., 2013). DMRs were then defined with R package DMRcaller (Catoni et al., 2018) as described before (Stroud et al., 2013) except that the 100bp window tested for DMR are 1kb flanking region over the 10776 ZF binding sites. DMRs within 200bp of each other were merged for further analysis. For analysis of hyperDMRs in DMS3-ZF, NRPD1-ZF or DMS3-ZF X NRPD1-ZF, all three types of hyperDMRs (CG/CHG/CHH) were combined and merged if the distance between two DMRs were less than 200bp. Annotations of hyperDMR to the nearest genes were calculated using HOMER (Heinz et al., 2010). In order to call high confidence CHH hyperDMR in DMS3-ZF fwa nrpd1 (Figure 6B), after calling genome-wide DMR, we filtered out DMRs with pre-existing CHH methylation greater than 0.05 as well as DMRs that overlapped with tRNA regions.
Genome_build: tair10
Supplementary_files_format_and_content: tab delimited text and bigwig
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| Submission date |
Jan 07, 2019 |
| Last update date |
Feb 07, 2019 |
| Contact name |
Wanlu Liu |
| Organization name |
Zhejiang University
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| Department |
Zhejiang University - University of Edinburgh Institute
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| Lab |
Wanlu Liu
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| Street address |
718 East Haizhou Rd.,
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| City |
Haining |
| State/province |
Zhejiang |
| ZIP/Postal code |
314400 |
| Country |
China |
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| Platform ID |
GPL13222 |
| Series (2) |
| GSE124546 |
Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis |
| GSE124746 |
Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis [WGBS] |
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| Relations |
| BioSample |
SAMN10702100 |
| SRA |
SRX5213730 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3553008_WGBS_fwa_FigureS1.CG.bw |
19.1 Mb |
(ftp)(http) |
BW |
| GSM3553008_WGBS_fwa_FigureS1.CHG.bw |
19.0 Mb |
(ftp)(http) |
BW |
| GSM3553008_WGBS_fwa_FigureS1.CHH.bw |
92.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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