|
| Status |
Public on Jan 30, 2023 |
| Title |
SH_ASF1A_set2_input |
| Sample type |
SRA |
| |
|
| Source name |
6-day-white-light grown seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedlings
genotype: 35S::ASF1A overexpression
treatment: 1 hr shade
chip antibody: GFP antibodies (ab290)
|
| Treatment protocol |
With 1 hr shade (white light as control) treatment.
|
| Growth protocol |
6-day-white-light grown seedlings were treated 1 hr shade before harvesting for DNA extraction using GFP antibodies.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was sonicated into fragments of 100-400 bp, followed by immuno-precipitation with anti-GFP.
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 |
| |
|
| 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: bigWig
|
| |
|
| Submission date |
Jan 09, 2023 |
| 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 |
SAMN32643873 |
| SRA |
SRX18980464 |
