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| Status |
Public on Mar 16, 2020 |
| Title |
Genome-wide maps of SMXL6 binding sites in Arabidopsis seedlings [pSMXL6:SMXL6-HA] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose: SMXL6 is a key repressor in strigolactone signaling. The goal of this study is to identify the targeted genes of SMXL6 in the model plant Arabidopsis thaliana.
Methods: The stable pSMXL6:SMXL6-HA transgenic line in the smxl6/7/8 background and the smxl6/7/8 mutant were grown for two weeks in 0.5 x MS medium and collected for extraction of the protein-DNA complexes. After ChIP analyses, DNA profiles were generated by deep sequencing, in double replicate, using Illumina system Novaseq 6000. The sequence reads were analyzed using BWA software and SAMtools. ChIP-qPCR validation was performed using Bio-Rad CFX 96 real-time PCR detection system.
Results: We identified 1665 and 1401 peaks in replicate experiment 1 and 2.
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| Overall design |
Investigating the binding sites of SMXL6 in the smxl6/7/8 pSMXL6:SMXL6-HA transgenic plants, using the smxl6/7/8 mutant as a control.
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| Contributor(s) |
Li J, Wang B |
| Citation(s) |
32528176 |
| Submission date |
Nov 19, 2019 |
| Last update date |
Jun 15, 2020 |
| Contact name |
Jiayang Li |
| E-mail(s) |
jyli@genetics.ac.cn
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| Organization name |
Institute of Genetics and Developmental Biology, CAS
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| Street address |
West Beichen Road
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| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA590540 |
| SRA |
SRP230651 |
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