|
| Status |
Public on Apr 28, 2017 |
| Title |
nrpd1_wgbs |
| Sample type |
SRA |
| |
|
| Source name |
2-week-old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: nrpd1-3
|
| Growth protocol |
On 1/2 MS plates at 22ºC with 12h:12h day-night cycle in the growth chamber
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted from 2-week-old seedlings using the Qiagen Plant DNeasy Maxi kit
Constructed using Illumina TruSeq DNA Library Prep Kit
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalling performed using CASAVA v1.8
Adapter sequences and low quality bases (q<30) removed using trim_galore v0.4.0 and catadapt v1.8.3
Reads aligned to the Arabidopsis TAIR10 genome using bsmap 2.74
Genome_build: TAIR10
Supplementary_files_format_and_content: tdf files of cytosine methylation ratio at single basepair resolution, only cytosines with a coverage > 4 are included
|
| |
|
| Submission date |
Apr 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Heng Zhang |
| E-mail(s) |
zhangheng@sibs.ac.cn
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Shanghai Center for Plant Stress Biology
|
| Street address |
3888 Chenhua Rd, Gate 3
|
| City |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE98283 |
The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci (Bisulfite-Seq) |
| GSE98286 |
The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci |
|
| Relations |
| BioSample |
SAMN06842155 |
| SRA |
SRX2766968 |
