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| Status |
Public on Apr 04, 2021 |
| Title |
Genome-wide mapping of OsHOX24-binding sites in rice |
| Organism |
Oryza sativa |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
In this study, we provide a global overview of genome-wide OsHOX24 binding sites in rice under control and desiccation stress conditions in wild-type and OsHOx24 overexpressing rice plants (H49 line) via chromatin immunoprecipitation sequencing (ChIP-sequencing) approach. We identified numerous downstream targets of OsHOX24 under desiccation stress and control by analyzing the comprehensive binding site map of OsHOX24 at whole genome level in rice.
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| Overall design |
We collected three-weeks-old seedlings of wild-type and OsHOX24 over-expression transgenic (H49 line) rice subjected to control (kept in water) and dessication (kept between folds of tissue paper) treatments for 3h. DNA was isolated from these tissue samples by chromatin immunoprecipitation and subjected to Illumina sequencing. The sequence data was then filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to rice genome sequence (MSU v7) using Bowtie2 software. MACS2 was used for peak calling and confident peaks were identified using Bedops pipeline. Several downstream targets of OsHOX24 were identified in rice under desiccation stress and control conditions.
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| Contributor(s) |
Jain M, Bhattacharjee A, Srivastava P, Tiwari O |
| Citation(s) |
33025523 |
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| Submission date |
Jan 28, 2020 |
| Last update date |
Jul 04, 2021 |
| Contact name |
Mukesh Jain |
| Phone |
91-11-26704686
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| Organization name |
Jawaharlal Nehru University
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| Street address |
New Mehrauli Road
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| City |
New Delhi |
| State/province |
New Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
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| Platforms (1) |
| GPL9316 |
Illumina Genome Analyzer II (Oryza sativa) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA603582 |
| SRA |
SRP245660 |
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