|
Status |
Public on Dec 20, 2021 |
Title |
βC1-OX-V17A-1/BSCTV-IR-Bisulfite-seq_rep2 |
Sample type |
SRA |
|
|
Source name |
leaves
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype: [beta]C1-OX-V17A-1 infection: BSCTV
|
Treatment protocol |
For TYLCCNV inoculation following VIGS, A. tumefaciens cultures carrying pCambia1300, pTRV1 plus pTRV2-GUS (TRV-GUS) or pTRV1 plus pTRV2-NbDMLs (TRV-NbDMLs) at an OD600 = 0.2 were inoculated into N. benthamiana plants at the eight-leaf stage. One week later, A. tumefaciens cultures harboring pBinPLUS (mock) or infectious clones of TYLCCNV or TYLCCNV plus TYLCCNB (TYLCCNV+B) at an OD600 = 1.0 were inoculated into pCambia1300-, TRV-GUS- or TRV-NbDMLs-infiltrated plants. For other TYLCCNV inoculation, N. benthamiana plants at the eight-leaf stage were directly agroinoculated with infectious clones of TYLCCNV, TYLCCNV+B or TYLCCNV+BV17A. Four-week-old A. thaliana were used for BSCTV inoculation as described before27. Symmetrically infected leaves were harvested at 10 days post inoculation.
|
Growth protocol |
N. benthamiana plants were grown in a controlled growth chamber at 25°C under a 16 h light/8 h dark photoperiod and A. thaliana plants were grown in a growth room under long photoperiod conditions (16 h light, 22°C/8 h dark, 18°C).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5042), according to the manufacturer’s instructions. The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)90. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).
|
|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
HiSeq X Ten |
|
|
Data processing |
PCR duplicated reads were removed and the unique reads with read counts above 5 were retained for cytosine methylation analysis Genome_build: TYLCCNV(AJ319675.1);BSCTV(U02311.1) Supplementary_files_format_and_content: the processed data files contain the unique sequence and their counts
|
|
|
Submission date |
Nov 16, 2021 |
Last update date |
Dec 21, 2021 |
Contact name |
Yijun Qi |
E-mail(s) |
qiyijun@mail.tsinghua.edu.cn
|
Organization name |
Tsinghua University
|
Department |
School of Life Sciences
|
Street address |
NO.1 Qinghuayuan
|
City |
Beiing |
ZIP/Postal code |
100084 |
Country |
China |
|
|
Platform ID |
GPL23157 |
Series (1) |
GSE188968 |
Geminiviruses employ host DNA glycosylases to subvert DNA methylation-mediated defense |
|
Relations |
BioSample |
SAMN23209595 |
SRA |
SRX13150382 |