|
| Status |
Public on Apr 01, 2023 |
| Title |
HTR5-HA |
| Sample type |
SRA |
| |
|
| Source name |
Col-0
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
cell line: Col-0
cell type: seedlings
chip antibody: anti-HA
|
| Growth protocol |
Arabidopsis thaliana seedlings were grown on MS medium under 16-h light/8-h dark conditions at 22°C for 14 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiment was referred to the previous study (PMID: 28138017).
ChIP-seq library construction was referred to the previously study (PMID: 31278262).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were trimmed to remove the adapters and take out the reads with low sequencing quality score using Cutadapt.
The trimmed reads were mapped to the Arabidopsis reference genome by Bowtie2 and the reads mapped to chloroplast or mitochondrial genomes were filtered.
SAMtools was used to remove reads with low mapping quality and potential PCR duplicates.
BamCoverage and computeMatrix tool in deepTools were used to calculate the enrichment level (RPKM) from 1kb upstream of the TSS to 1kb downstream of the TTS.
Average density profile was plotted in R and a heatmap was generated using the plotHeatmap tool in deepTools.
SICER was used to find peaks and differentially enriched peaks.
Assembly: TAIR10
Supplementary files format and content: bigwig
|
| |
|
| Submission date |
Jan 19, 2023 |
| Last update date |
Apr 02, 2023 |
| Contact name |
Jiachen Wang |
| E-mail(s) |
[email protected]
|
| Phone |
+86-13204722665
|
| Organization name |
Fudan University
|
| Department |
Institute of Plant Biology
|
| Street address |
No. 2005, Songhu Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE223308 |
ChIP-seq for HA-HTR5/Col-0 and Col-0 using HA antibody |
|
| Relations |
| BioSample |
SAMN32802078 |
| SRA |
SRX19085871 |
