|
| Status |
Public on Feb 05, 2015 |
| Title |
nrpd1-3_MethylC-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: nrpd1-3 mutant
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 14-d-old seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
treated with bisulfite
|
| Data processing |
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (converted_C / ( converted_C+ unconverted_C ) ).
|
| |
|
| Submission date |
Dec 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
zhu132@purdue.edu
|
| Organization name |
Purdue University
|
| Department |
Department of Horticulture and Landscape Architecture
|
| Street address |
625 Agriculture Mall Dr.
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE64499 |
MethlyC-Seq of nrpd1-3, nrpd1-12, and nrpe1-11 |
|
| Relations |
| BioSample |
SAMN03273107 |
| SRA |
SRX823947 |
| Named Annotation |
GSM1572728_nrpd1-3B_rep2_NCBI_depth4_mCG.wig.gz |
| Named Annotation |
GSM1572728_nrpd1-3B_rep2_NCBI_depth4_mCHG.wig.gz |
| Named Annotation |
GSM1572728_nrpd1-3B_rep2_NCBI_depth4_mCHH.wig.gz |
