|
| Status |
Public on Dec 01, 2018 |
| Title |
Mock [MethylC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
inflorescences
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
tissue: Inflorescences
age: 6-weeks-old
agent: none
|
| Treatment protocol |
Arabidopsis plants were inoculated on rosette leaves using fresh inoculum prepared from Nicotiana benthamiana leaves systemically infected with an infectious TRV-GFP clone
|
| Growth protocol |
Arabidopsis thaliana plants were grown in controlled environment chambers under 16 h/8 h of light/dark at 22ºC
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Arabidopsis inflorescences were collected at 14dpi and frozen on liquid nitrogen and genomic DNA (gDNA) was extracted using DNeasy Plant Mini kit (Qiagen). For mock-samples, the same procedure was performed at 6-weeks-old Arabidopsis plants.
Library construction and Whole Genome Bisulphite sequencing (WGBS) were done by BGI-Tech on Illumina HiSeq2000
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads by using BGI programs (Liang et al., 2014)
Clean data were aligned to the reference genome TAIR10 by BSMAP with the following parameters: bsmap -a filename_1.clean.fq.gz -b filename_2.clean.fq.gz -o filename.sam -d ref.fa -u -v -z 33 -p 4 n0 -w 20 -s 16 -f 10 -L 90
DMR were identified by comparison of the sample1 and sample2 methylomes using windows that contained at least 5CpG (CHG or CHH) sites with a 2-fold change in methylation level and Fisher test p value <= 0.05.
The degree of difference of a methyl-cytosine (mCG, mCHG, mCHH) between samples was calculated by comparing methylation level of DRM of sample1 and sample2 by CIRCOS.
Genome_build: TAIR 10 Arabidosis thaliana genome
Supplementary_files_format_and_content: Mapping Rate: Mapping_Rate.xls
Supplementary_files_format_and_content: Table 1_mC abundance: Abundance of methylated cytosines in the three possible contexts in TRV-infected and mock-inoculated Arabidopsis inflorescences at 14 dpi.
Supplementary_files_format_and_content: Table 2_genome wide mC: Average genome-wide methylation levels of coding genes at the three possible cytosine contexts
Supplementary_files_format_and_content: Table 3_DMRs: Identification of differentially methylated regions (DMR) in which DNA methylation levels varied significantly between TRV-infected and mock-inoculated Arabidopsis inflorescences at 14 dpi.
|
| |
|
| Submission date |
Jul 20, 2018 |
| Last update date |
Dec 01, 2018 |
| Contact name |
Virginia Ruiz-Ferrer |
| E-mail(s) |
vruizferrer@cib.csic.es
|
| Phone |
+34 91 837 31 12
|
| Organization name |
CSIC
|
| Department |
Environmental Biology
|
| Lab |
Stress and Gene Regulation
|
| Street address |
Ramiro de Maeztu, 9
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE117418 |
Next Generation Sequencing Facilitates Quantitative Analysis of mock and tobacco ratle virus (TRV) Arabidopsis inflorescences Methylome. [MethylC-seq] |
| GSE117419 |
Next Generation Sequencing Facilitates Quantitative Analysis of mock and tobacco ratle virus (TRV) Arabidopsis inflorescences Transcriptome |
|
| Relations |
| BioSample |
SAMN09709324 |
| SRA |
SRX4452396 |
