|
| Status |
Public on Jun 30, 2023 |
| Title |
Red-TM29-plateA-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
AC fruit
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: fruit
cultivar: Ailsa Craig
dna library: 100ng
batches: plateA
Stage: Red
tag: HALO
|
| Treatment protocol |
None
|
| Growth protocol |
Plants were grown in green house under normal condition (26℃, 70% humidity,14h light, 10h dark).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Plant DNAZOL® Reagent.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
A23-1
DAP-seq of TM29 incubated with DNA library extracted from tomato AC 38 DPA fruit in plateA
Red-TM29-plateA_peaks_p15fc5.txt
|
| Data processing |
Library strategy: DAP-seq
Fastq files were trimmed using fastp.
Clean reads were mapped to tomato build 4.0 genome using bowtie2 version 2.3.4.1 with default parameters.
Reads were filtered using samtools '-f 2 -q 20 '.
GATK MarkDuplicates tool was used to remove duplication.
Peak calling for TFs was performed by macs2; Peak calling for MBD5 was performed by SICER.
Genome_build: SL4.0
Supplementary_files_format_and_content: bigWig files were generated using tool bamCoverage.
Supplementary_files_format_and_content: bed, txt files include peaks.
|
| |
|
| Submission date |
Apr 16, 2021 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Yu Ma |
| E-mail(s) |
yuma@psc.ac.cn
|
| Organization name |
Shanghai Center for Plant Stress Biology
|
| Street address |
Address: No. 3888 Chenhua Road, Shanghai 201602, P. R. China
|
| City |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL29032 |
| Series (2) |
| GSE172260 |
Comprehensive characterization of cistrome and epicistrome involved in fruit ripening [red fruit] |
| GSE173213 |
Comprehensive characterization of cistrome and epicistrome involved in fruit ripening |
|
| Relations |
| BioSample |
SAMN18779345 |
| SRA |
SRX10624306 |
