|
| Status |
Public on Feb 14, 2023 |
| Title |
vil1 22°C H3K27me3 ChIP-seq input |
| Sample type |
SRA |
| |
|
| Source name |
Seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Seedling
genotype: vil1-1
temperature: 22degreeC
age: 7 days
chip antibody: None
|
| Treatment protocol |
Plants were grown in short day (8-hour light, 16-hour dark) at 22°C or 27°C.
|
| Growth protocol |
Tissue (7-day-old seedlings) was harvested for experiment at ZT-6.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments.
Library was prepared using NEB Illumina library preparation kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
vil1_22C_input.bw
|
| Data processing |
Reads generated by Illumina NextSeq 500 platform were checked for quality using FastQC.
After quality assessment, reads were aligned on TAIR10 genome using Bowtie2 for ChIP-seq.
SAM files generated from mapping were then converted into BAM files and sorted using Samtools.
For the gene counting bedtools program was used which generates raw count using BAM files.
Genome_build: TAIR10
Supplementary_files_format_and_content: .bw (IGV)
|
| |
|
| Submission date |
Sep 07, 2021 |
| Last update date |
Feb 14, 2023 |
| Contact name |
Sibum Sung |
| E-mail(s) |
sbsung@austin.utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Street address |
NMS 5.110, Stop A5000
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE149686 |
Warm temperature-triggered developmental reprogramming requires VIL1-mediated, genome-wide H3K27me3 accumulation in Arabidopsis |
|
| Relations |
| BioSample |
SAMN21341738 |
| SRA |
SRX12075524 |
