|
| Status |
Public on Dec 01, 2020 |
| Title |
WT-ChIP-3 |
| Sample type |
SRA |
| |
|
| Source name |
fruit pericarp
|
| Organism |
Solanum lycopersicum |
| Characteristics |
development stage: 38 dpa
tissue: fruit pericarp
genotype: wild type
antibody: anti-DOF1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The enriched nuclei were sonicated to fragment DNA to 250-500 bp and the sheared chromatin was incubated with the anti-DOF1 antibody.The immunoprecipitated DNA and input DNA were purified with phenol/chloroform extraction.
Libraries was prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina GA Pipeline v1.5 software used for basecalling.
Raw sequence reads were filtered for adaptor sequence, unknown base more than 10% and low-quaility reads.
Filtered clean reads were mapped to tomato whole genome using SOAPaligner/SOAP2 software with parameter SOAPnuke filter -l 20 -q 0.5 -n 0.1 -i -c 25
Uniquely mapped reads were submitted to MACS Version 1.4.2 to call the enriched peaks with default parameter.
Genome_build: ITAG, the International Tomato Annotation Group release version 2.5
Supplementary_files_format_and_content: Wg files includes peak location, peak length, etc.
|
| |
|
| Submission date |
Sep 05, 2018 |
| Last update date |
Dec 02, 2020 |
| Contact name |
Yuying Wang |
| E-mail(s) |
41783425@qq.com
|
| Organization name |
Institute of botany, the chinese academy of sciences
|
| Street address |
No.20 Nanxincun, Xiangshan
|
| City |
Beijing |
| ZIP/Postal code |
100093 |
| Country |
China |
| |
|
| Platform ID |
GPL16345 |
| Series (2) |
| GSE119492 |
Genome-wide binding analysis of SlDof1 in tomato fruit |
| GSE119565 |
Regulatory network of SlDof1 in fruit ripening |
|
| Relations |
| BioSample |
SAMN09976774 |
| SRA |
SRX4643711 |
