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| Status |
Public on Nov 22, 2022 |
| Title |
BYSR-input |
| Sample type |
SRA |
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| Source name |
cells
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| Organism |
Burkholderia sp. JP2-270 |
| Characteristics |
strain: JP2-270
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DAP-seq was carried out in duplicate on Burkholderia sp. JP2-270 genomic DNA. Specifically, the Halo-BysR protein was expressed using the TNT SP6 Wheat Germ Protein Expression System (Promega, Fitchburg, WI, USA). The Halo Tag-BysR protein was purified using magnetic HaloTag beads (Promega) and verified by Western blotting with the anti-HaloTag antibody (Promega).
Genomic DNA was extracted from JP2-270 using DNAiso (Takara, Japan). Genomic DNA library was generated using NEXTflex Rapid DNA Seq kit (Bioo Scientific, USA) following the manufacturer’s instructions. The purified protein was incubated with DNA library at 30 ° C for 2 h, and then the unbound DNA fragments was washed away. Then, the BysR-bound DNA fragments were recovered and PCR-amplified. The resultant products were sequenced using the Illumina NovaSeq platform with the sequencing strategy of PE150.
DAP-seq
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Basecalls performed using CASAVA version 1.4
The clean reads were obtained by filtering the raw data using FASTP with the default parameters. The clean reads were mapped to the Burkholderia sp. JP2-270 reference genome (CP029824-CP029828) using BWA-MEM.
Peaks were generated with MACS2 with the following setting: p-value (0.05), Enrichment Fold (1).IDR (Li et al., 2011) software was used to merge peaks of two technical repeated samples, and the reliability of repeated peak was scored.
Genome_build: NCBI accession number: CP029824-CP029828
Supplementary_files_format_and_content: peak text files
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| Submission date |
Jan 18, 2022 |
| Last update date |
Nov 23, 2022 |
| Contact name |
Lijuan Wu |
| E-mail(s) |
[email protected]
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| Organization name |
China national rice research institute
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| Street address |
28 Shui Dao Suo Road, Fuyang District
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
311400 |
| Country |
China |
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| Platform ID |
GPL31243 |
| Series (1) |
| GSE193916 |
Genome wide identification of BysR binding sites in Burkholderia sp. JP2-270 |
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| Relations |
| BioSample |
SAMN25068018 |
| SRA |
SRX13822876 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5823598_BYSR-input.wig.gz |
1.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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