|
| Status |
Public on Nov 06, 2024 |
| Title |
WGBS hda6/ldl1/2 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: 14 days seedling
ecotype: Col-0
tissue: seedling
genotype: hda6/ldl1/2
|
| Growth protocol |
Arabidopsis was grown in growth chambers under 12/12 h light/dark conditions at 22°C and harvested after 14 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA were extracted by grinding in liquid nitrogen followed by purification with Dneasy Plant Mini Kit (Qiagen)
Genomic DNA was extracted from 14-d-old seedlings of Col-0, hda6, ldl1/2, and hda6/ldl1/2 using a DNeasy Plant Mini Kit (Qiagen). After quality assessment, 200 ng genomic DNA was sheared using Covaris and used to make libraries using Nugen Ultralow Methyl-seq kit (Ovation) according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
BS-seq reads were trimmed (removing sequencing adapter and low-quality reads) by using Trimmomatic.
High-quality clean BS-seq reads were aligned to the Arabidopsis reference genome (TAIR10) using BS-Seeker2.
Assembly: TAIR10
Supplementary files format and content: Processed data (CGmap) is in text format. column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.
|
| |
|
| Submission date |
Oct 28, 2022 |
| Last update date |
Nov 06, 2024 |
| Contact name |
Pao-Yang Chen |
| Organization name |
Academia Sinica
|
| Department |
Institute of Plant and Microbial Biology
|
| Lab |
Pao-Yang Chen
|
| Street address |
128 Sec. 2, Academia Rd, Nankang,
|
| City |
Taipei |
| ZIP/Postal code |
115 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL23157 |
| Series (2) |
| GSE216787 |
Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 [WGBS] |
| GSE216789 |
Epigenetic-driven Synergistic and Antagonistic regulation on Transposable Elements Carried Out by HDA6 and LDL1/2 |
|
| Relations |
| BioSample |
SAMN31507277 |
| SRA |
SRX18061846 |
