|
| Status |
Public on Sep 28, 2022 |
| Title |
Col-Input-24h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Col 24h imbibed seeds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col
genotype: wild type
chip antibody: none
|
| Growth protocol |
After-ripened Col and ref6c seeds (seeds harvested and stored at room temperature for at least three months) collected at the same time and growth conditions were sown on 1/2 MS medium, and subsequently subjected for germination in long days at ~22°C, and collected at different imbibition time points.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Materials were ground with liquid nitrogen into fine powder and fixed with 1% formaldehyde. To profile H3K27me3, nuclei were extracted and mononucleosomes were generated with micrococcal nuclease (MNase)(Sigma, N5386) digestion. Immunoprecipitation was conducted with anti-H3K27me3 antibody (Merck, 07-449). After antibody incubation, Protein A Dynabeads (Life technologies, 10002D) were added to collect the immunocomplexes, followed by elution, reverse cross-linking and DNA purification.
Library was prepared with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607) according to the manufacture’s instruction
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapter trimming was performed and low-quality reads were filtered with fastp version 0.20.1
Reads were mapped to the Arabidopsis genome (TAIR10) with Botiew2 version 2.4.2
Duplicated reads were filtered using Picard version 2.24.0 MarkDuplicates (https://github.com/broadinstitute/picard).
The correlation coefficients between biological replicates were examined using deepTools version 3.1.3 utility multiBamSummary, and subsequently biological replicates were merged with SAMtools version 1.9
For data visualization, bigwig coverage files were generated using deepTools utility bamCoverage with a bin size of 10bp and normalized to sequencing depth using RPKM
ChIP-seq peaks were identified using MACS2 version 2.1.2 with default parameters. The parameter ‘--broad’ was used for the calling of H3K27me3 peaks. The q-value cutoff for peak calling was 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: *.bw: Normalized H3K27me3 coverage files. Data is generated from merged replicates
|
| |
|
| Submission date |
Jun 01, 2021 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Jie Pan |
| E-mail(s) |
jpan@genetics.ac.cn
|
| Organization name |
Institute of Genetics and Developmental Biology
|
| Street address |
No.1 West Beichen Road,Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (2) |
| GSE167503 |
A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [H3K27me3 ChIP-seq] |
| GSE167508 |
A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis |
|
| Relations |
| BioSample |
SAMN19486911 |
| SRA |
SRX11037816 |
