|
| Status |
Public on Dec 29, 2016 |
| Title |
Col-0 |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: WT
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The genomic DNA was extracted from 1 gram of 14-day-old seedlings using the Plant DNeasy Maxi Kit from Qiagen. And 5 µg of gDNA was used for library construction using Illumina’s standard DNA methylation analyses protocol and the TruSeq DNA sample preparation kit. The samples were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq2500.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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 ( unconverted_C / ( converted_C+ unconverted_C ) ).
|
| |
|
| Submission date |
Oct 28, 2016 |
| 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 |
GPL17639 |
| Series (2) |
| GSE89294 |
Whole genome bisulfite sequencing of hdp1-1 and hdp2-1and other relative mutants (Col-0 background) |
| GSE89320 |
A Pair of Transposon-derived Proteins Function in A Histone Acetyltransferase Complex for Active DNA Demethylation |
|
| Relations |
| BioSample |
SAMN05954300 |
| SRA |
SRX2310515 |
