|
| Status |
Public on Mar 06, 2024 |
| Title |
v1c1_3 |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings, short day, ZT0, rep3
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedling
cell type: plant cell
genotype: vil1-1cop1-4
chip antibody: H3K27me3 (Active Motif #39155)
|
| Treatment protocol |
Short day conditions (8-h light, 16-h dark) at 22°C for a week, samples collected at ZT0
|
| Growth protocol |
Seedlings were germinated and grown on MS medium in short day condition for a week
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor (30 s on/2 min 30 s off cycles) with high-power output to obtain 200- to 500-bp DNA fragments.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality check using FastQC
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30
Reads were aligned on the TAIR10 genome using Bowtie2
SAM files generated from mapping were then converted into BAM files and sorted using Samtools.
Bigwig files for IGV visualization were created using deeptools
Assembly: TAIR10
Supplementary files format and content: bigWig, Peak
|
| |
|
| Submission date |
May 23, 2023 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Wenli Wang |
| E-mail(s) |
wenli7898@gmail.com
|
| Phone |
7376150810
|
| Organization name |
university of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Lab |
Sung lab
|
| Street address |
2506 Speedway NMS 5.268, NMS 5.268
|
| City |
Austin |
| State/province |
Texas |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE233271 |
COP1 controls light-dependent chromatin remodeling in Arabidopsis [ChIP-Seq] |
| GSE233273 |
COP1 controls light-dependent chromatin remodeling in Arabidopsis |
|
| Relations |
| BioSample |
SAMN35340264 |
| SRA |
SRX20496142 |
