|
| Status |
Public on Jul 19, 2023 |
| Title |
IP_JA-1 |
| Sample type |
SRA |
| |
|
| Source name |
6-day-old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
treatment: treated with 5-µm JA
material type: LHP1:Flag
ecotype: Col-0
experiment: IP
|
| Treatment protocol |
6-d-old seedlings was treated with 5-µm JA for 3 hr
|
| Growth protocol |
seedlings grown in liquid half-strength MS media supplemented with 1% sucrose
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted from liquid-cultured LHP1:Flag seedlings as previously described (Louwers et al., 2009), followed by chromatin immunoprecipitation with anti-Flag M2 magnetic beads (Sigma).
DNA libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw paired-end reads (21 to 26 million per sample) were cleaned by Trimimomatic , to trim the adapter sequences, remove low-quality bases and filter short reads (< 36 nt)
Clean reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 (version 2.2.8) with default parameters. Mapped reads with low mapping quality (MAPQ < 30) or multiple positions in the genome were removed by SAMtools(version 1.3) .
Enriched peaks were identified by MACS2 (version 2.2.7.1, with a cut-off p value 0.01.
We defined the region of a target gene as the range from 1kb upstream of transcription start site (TSS) to transcription end site (TES). The target genes of each peak were annotated by annotatePeak function in ChIPseeker package.
The visualization of the average read coverage over gene body and additional 0.5/1kb up- and down-stream of the TSS and TES was performed by deepTools (version 2.4.1). The read coverage of individual genes was visualized with the Gviz package.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedgraph with peak score
|
| |
|
| Submission date |
Feb 26, 2021 |
| Last update date |
Jul 19, 2023 |
| Contact name |
li peng |
| E-mail(s) |
[email protected]
|
| Phone |
18721062615
|
| Organization name |
PSC
|
| Street address |
NO.38888,chenhualu
|
| City |
shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (2) |
| GSE167636 |
JASMONATE-ZIM DOMAIN proteins engage Polycomb chromatin modifiers to modulate Jasmonate signaling in Arabidopsis [ChIP-Seq] |
| GSE167639 |
JASMONATE-ZIM DOMAIN proteins engage Polycomb chromatin modifiers to modulate Jasmonate signaling in Arabidopsis |
|
| Relations |
| BioSample |
SAMN18070358 |
| SRA |
SRX10176141 |
