|
| Status |
Public on Sep 06, 2024 |
| Title |
clf-0-1-Input |
| Sample type |
SRA |
| |
|
| Source name |
clf_Untreated
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: clf
treatment: Untreated
time point: 0hpi
chip antibody: none
|
| Treatment protocol |
Four-week-old Arabidopsis plant leaves were treated in growth chambers, with relative humidity about 95% and temperature at 22℃ with 12/12h day/night photoperiod.
|
| Growth protocol |
Plants were grown in soil in environmentally-controlled growth chambers, with relative humidity at 60% and temperature at 22℃ with 12/12h day/night photoperiod.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27me3 antibody.
Libraries were prepared according to Novogene Corporation (Beijing, China) protocols.Subsequently, pair-end sequencing of samples was performed on Illumuna platform (Illumina, CA, USA)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
clf-0-1-Input_FMRC202438993-1a
|
| Data processing |
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to TAIR RefSeq v10 using BWA 0.7.5a-r405 for ChIP-seq, all with default settings.
For ChIP-seq, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–5 and fold-change >32. ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
Genome_build: TAIR 10
Supplementary_files_format_and_content: Peak files and bigwig files were provided.
|
| |
|
| Submission date |
Sep 07, 2021 |
| Last update date |
Sep 06, 2024 |
| Contact name |
Minhang Yuan |
| E-mail(s) |
mhyuan@sibs.ac.cn
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Shanghai Institute of Plant Physiology and Ecology
|
| Lab |
Plant-microbe Interactions
|
| Street address |
Fenglin
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (2) |
| GSE183557 |
Genome-wide histone 3 lysine 27 trimethylation patterns in wild type and CLF-deficient Arabidopsis plants after high humidity treatment [ChIP-seq] |
| GSE183559 |
Genome-wide histone 3 lysine 27 trimethylation patterns and expression analysis of WT and CLF-deficient Arabidopsis plants after high humidity treatment |
|
| Relations |
| BioSample |
SAMN21250524 |
| SRA |
SRX12030239 |
