|
| Status |
Public on Aug 03, 2022 |
| Title |
WUSCHEL_input |
| Sample type |
SRA |
| |
|
| Source name |
Ailsa Craig
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: Ailsa Craig
cell line: flower abscission zone
cell type: Halo
|
| Growth protocol |
greenhouse (16 h of light at 25°C, 8 h of dark at 15°C)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The DAP genomic DNA (gDNA) library was prepared using the kit from NEBNext® DNA Library Prep Master Mix Set for Illumina
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
DAP-seq reads were aligned to the Tomato Genome version SL4.0 (https://solgenomics.net/organism/Solanum_lycopersicum/genome) using Bowtie2 (version:2.2.5).
MACS2 (version:2.1.2) software was used to identify read-enriched regions from the DAP-seq data.
Peak-related genes were annotated using the CHIPseeker R package
The MEME suite (http://meme-suite.org/) was used to detect motifs
MEME (http://meme-suite.org/tools/meme) and DREME (http://meme-suite.org/tools/dreme) were used to detect long and short consensus sequences, respectively.
Supplementary files format and content: SL4.0
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: DAP-Seq
|
| |
|
| Submission date |
Jul 31, 2022 |
| Last update date |
Aug 03, 2022 |
| Contact name |
lina cheng |
| Organization name |
shenyang agriculture university
|
| Department |
college of Horticulture
|
| Street address |
dongling road NO.120
|
| City |
shenyang |
| ZIP/Postal code |
110866 |
| Country |
China |
| |
|
| Platform ID |
GPL25655 |
| Series (1) |
| GSE210149 |
A SlCLV3-SlWUS module regulates auxin and ethylene homeostasis in low light–induced tomato flower abscission |
|
| Relations |
| BioSample |
SAMN30072286 |
| SRA |
SRX16747794 |
