|
| Status |
Public on Aug 17, 2018 |
| Title |
WT_H3_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
seedling tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cell type: developmental stage
antibody: H3
catalog#/vendor: abcam1791 (Abcam)
genotype/variation: wild type
|
| Growth protocol |
Plants were grown under constant light at 22 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were crosslinked in vitro, sheared using a Bioruptor Plus (Diagenode), chromatin was then split for each sample.
Libraries generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions, proceeding from step F (DNA purification) and were sequenced on an Illumina HiSeq 4000 instrument.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
ChIP-seq reads were aligned to the tair10 genome assembly using Bowtie (v1.1.2): bowtie -q -v 0 -p 8 -S -m 1
Bam files were deduplicated with samtools: samtools rmdup
Differential peaks were called by bdgdiff function in MACS2.
ChIP-seq data metaplots were plotted by deeptools (v2.5.1)
Genome_build: tair10
Supplementary_files_format_and_content: wig
|
| |
|
| Submission date |
May 03, 2018 |
| Last update date |
Aug 19, 2018 |
| Contact name |
Zhenhui Zhong |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE114009 |
Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation |
|
| Relations |
| BioSample |
SAMN09059720 |
| SRA |
SRX4036321 |
