|
| Status |
Public on Jan 30, 2023 |
| Title |
WL_HTR5_pif7_set2_input |
| Sample type |
SRA |
| |
|
| Source name |
8-day-old white light-grown pHTR5::HTR5-HA /pif7-1 seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedlings
cell type: whole seedlings
|
| Treatment protocol |
With 1 hr shade (white light as control) treatment
|
| Growth protocol |
8-day-white-light grown seedlings were treated 1 hr shade before harvesting for pHTR5::HTR5-HA/pif7-1 DNA extraction using HA antibodies.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was sonicated into fragments of 100-400 bp, followed by immuno-precipitation with anti-HA.
DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WL_HTR5_pif7_input.bw
|
| Data processing |
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to Tair10 using STAR
Read counts were calculated by using htseq-count
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Assembly: Tair 10
Supplementary files format and content: BW
|
| |
|
| Submission date |
Sep 12, 2022 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Chuanwei Yang |
| E-mail(s) |
yangchuanwei@fudan.edu.cn
|
| Organization name |
Fudan university
|
| Department |
school of life sciences
|
| Street address |
2005 Songhu Road, Yangpu District
|
| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE193955 |
PHYTOCHROME-INTERACTING FACTOR 7-mediated epigenetic reprogramming promotes the transcriptional response to shade in Arabidopsis |
|
| Relations |
| BioSample |
SAMN30808982 |
| SRA |
SRX17535119 |
