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| Status |
Public on May 08, 2023 |
| Title |
ddr4_rep2_WGBS |
| Sample type |
SRA |
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| Source name |
seedling
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedling
cell line: seedling
cell type: seedling
genotype: ddr4
treatment: ddr4
time: DAY 10
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
10-day-old seedlings were collected for DNA extraction using a CTAB-based method. 400 ng DNA was used for bisulfite conversion with the EZ DNA methylation-lighting kit
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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 |
Adaptors were first trimmed from the raw sequencing reads using fastp v0.20.1. The trimmed reads were aligned to TAIR10 reference genome using BSMAP v2.90 under default settings (-v 2, allowing up to 2 mismatches; -w 1, report the best hit; -n 1, aligning to both strands). Reads with more than three consecutive methylated CHH were removed as described previously. The methratio.py script from the BSMAP package was used to extract the number of methylated cytosine at single base pair resolution.
Assembly: TAIR10
Supplementary files format and content: The processed data is generated by the BSMAP methratio.py script.
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| Submission date |
Mar 10, 2023 |
| Last update date |
May 08, 2023 |
| Contact name |
Zejia Wang |
| E-mail(s) |
wangzj@stu.pku.edu.cn
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| Organization name |
Peking University
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| Street address |
Yanyuan Street
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL26208 |
| Series (2) |
| GSE202270 |
DDT-RELATED PROTEIN4-IMITATION SWITCH alters nucleosome distribution to relieve transcriptional silencing in Arabidopsis [Bisulfite-seq] |
| GSE202271 |
DDT-RELATED PROTEIN4-IMITATION SWITCH alters nucleosome distribution to relieve transcriptional silencing in Arabidopsis |
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| Relations |
| BioSample |
SAMN33713711 |
| SRA |
SRX19633846 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7091061_ddr4_rep2.txt.gz |
290.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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