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| Status |
Public on Nov 01, 2016 |
| Title |
K21_nrpd1_MethylC-Seq |
| Sample type |
SRA |
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| Source name |
Seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: nrpd1-3
tissue: seedling
age: 14 days old
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 14-d-old seedlings and sent to Genomics Core Facility of Shanghai Center for Plant Stress Biology for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
treated with bisulfite
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| 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 ) ).
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| Submission date |
Aug 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
zhu132@purdue.edu
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| Organization name |
Purdue University
|
| Department |
Department of Horticulture and Landscape Architecture
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| Street address |
625 Agriculture Mall Dr.
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| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platform ID |
GPL13222 |
| Series (2) |
| GSE72280 |
MethlyC-Seq of Col-0 (wild type, WT), nrpd1-3, nrpe1-11, ros1-4 single mutants and ros1-4nrpd1-3 double mutant |
| GSE83802 |
The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications |
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| Relations |
| BioSample |
SAMN04008888 |
| SRA |
SRX1162564 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1859476_K21_nrpd1_combined_NCBI_depth4_mCG.wig.gz |
15.1 Mb |
(ftp)(http) |
WIG |
| GSM1859476_K21_nrpd1_combined_NCBI_depth4_mCHG.wig.gz |
15.4 Mb |
(ftp)(http) |
WIG |
| GSM1859476_K21_nrpd1_combined_NCBI_depth4_mCHH.wig.gz |
69.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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