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Status |
Public on Oct 07, 2020 |
Title |
50ng-12PCR-WGBS_replicate2 |
Sample type |
SRA |
|
|
Source name |
50ng-12PCR-WGBS
|
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.
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
50ng-12PCR-WGBS_replicate2_meth
|
Data processing |
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
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|
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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 |
SAMN15081332 |
SRA |
SRX8453212 |