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Sample GSM5692653 Query DataSets for GSM5692653
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

Supplementary file Size Download File type/resource
GSM5692653___C1-V17A-OX-1Rep2.uni.tar.gz 43.6 Kb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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