|
| Status |
Public on Oct 27, 2022 |
| Title |
ZF-ASF1B_H3.3_myc_ChIPseq_DNA_input |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis floral tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: floral tissue
developmental stage: 5-6 weeks
strain: Columbia-0
antibody: anti-myc
target protein: H3.3
|
| Growth protocol |
Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). Floral tissues were collected from 5-6 week plants
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seeq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ChIP-seq data of H3.3 myc in ZF-ASF1B DNA input
|
| Data processing |
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
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)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T). Differential Methylated Regions (DMRs) were called by methdiff function with every 100bp bin for where the difference in CG, CHG, and CHH methylation are at least 0.4, 0.2, and 0.1, respectively.
Assembly: tair10
Supplementary files format and content: bigWig
Supplementary files format and content: peak
|
| |
|
| Submission date |
Aug 05, 2022 |
| Last update date |
Nov 29, 2022 |
| 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 |
GPL21785 |
| Series (1) |
| GSE188493 |
Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis |
|
| Relations |
| BioSample |
SAMN30169692 |
| SRA |
SRX16890149 |
