|
| Status |
Public on Oct 07, 2020 |
| Title |
400ng-18PCR-EM_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
400ng-18PCR-EM
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia-0
developmental stage: 4 weeks
tissue: flowers
|
| Growth protocol |
Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown at 22 °C in a long day (16 hour light, 8 hour dark) growth room. Flowers and leaves were collected from 4-5 week-old plants.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from Arabidopsis flowers and leaves was extracted using DNeasy Plant Mini Kit (Qiagen). Concentration of the DNA was measured by Qubit dsDNA Broad-Range Assay kit (ThermoFisher). 50 μl aliquots containing 25, 50, 150, and 400 ng DNA were sheared by an S2 Focused-ultrasonicator (Covaris) to ~200 bp in average size using these parameters: intensity 5, duty cycle 10%, cycles per burst 200, and treatment time 120 sec.
EM-Seq libraries were prepared from sheared DNA using Enzymatic Methyl-seq kit following manufacturer instructions (New England BioLabs). For each input amount, three PCR conditions were used: 6, 12, and 18 cycles. Sheared DNA was end-repaired and ligated with TruSeq DNA single adapters (Illumina) using Kapa DNA HyperPrep kit (Roche). Adapter-ligated DNA was converted by EpiTect Bisulfite Kit (Qiagen). And converted DNA was amplified by MyTaq polymerase (Bioline) for 6, 12, or 18 cycles.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
400ng-18PCR-EM_replicate1_meth
|
| Data processing |
library strategy: EM-seq
BS-seq reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1).
Reads with three or more consecutive methylated CHH sites were considered as “unconverted” and subsequently removed.
DNA methylation levels were calculated by #C/ (#C + #T).
Genome_build: tair10
Supplementary_files_format_and_content: bigWig: methylome profile
|
| |
|
| Submission date |
Jun 02, 2020 |
| Last update date |
Oct 08, 2020 |
| Contact name |
Zhenhui Zhong |
| E-mail(s) |
zhenhuizhong@gmail.com
|
| Organization name |
University of California, Los Angeles
|
| Department |
Department of Molecular, Cell and Developmental Biology
|
| Lab |
Jacobsen Lab
|
| Street address |
610 Charles E Young Dr East
|
| City |
Los Angeles |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE151616 |
Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing |
|
| Relations |
| BioSample |
SAMN15081220 |
| SRA |
SRX8453183 |
