 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 12, 2021 |
| Title |
fve_rep1 [Bisulfite-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: fve(-/-)
tissue: seedlings
age: 11 days
|
| Treatment protocol |
The 11-day-old seedlings grown on MS plates were harvested and subjected to DNA extraction.
|
| Growth protocol |
Arabidopsis seedlings were grown on MS medium plates with 16 h of light at 23ºC and 8 h of darkness at 21ºC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 11-day-old Arabidopsis seedlings by CTAB and purified with phenol: chloroform (1:1).
DNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls performed using bcl2fastq version 2.16.
For analysis of whole-genome DNA methylation data, the mapping, duplication filtering, and methylation extracting were all performed using the standard procedure of Bismark (v0.22.3).
The clean reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie2 and allowing one mismatch.
After duplications were removed, DNA methylation at CG, CHG, and CHH sites were calculated separately.
For the identification of different types of DMRs, the genome was divided in 200-bp bins, and the CG, CHG, and CHH methylation levels in each bin were calculated and compared between the WT and the mutants. Bins that showed differences in DNA methylation levels (CG > 0.4, CHG > 0.2, CHH > 0.1) were recorded and filtered based on Fisher’s exact test and BH method adjusted p values (cutoff = 0.01).
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig format files for each cytosine context (CG, CHG, CHH or CX) with the following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level.
|
| |
|
| Submission date |
Mar 18, 2021 |
| Last update date |
Jun 12, 2021 |
| Contact name |
xinjian He |
| E-mail(s) |
hexinjian@nibs.ac.cn
|
| Organization name |
National Institute of Biological Sciences
|
| Lab |
hexinjian
|
| Street address |
No. 7, zhongguancun life science park road, changping district
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (2) |
| GSE169178 |
FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin [Bisulfite-seq] |
| GSE169180 |
FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin |
|
| Relations |
| BioSample |
SAMN18352165 |
| SRA |
SRX10379046 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5179586_fve_rep1_CG.bw |
34.2 Mb |
(ftp)(http) |
BW |
| GSM5179586_fve_rep1_CHG.bw |
37.3 Mb |
(ftp)(http) |
BW |
| GSM5179586_fve_rep1_CHH.bw |
159.6 Mb |
(ftp)(http) |
BW |
| GSM5179586_fve_rep1_CX.bw |
208.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
