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| Status |
Public on Sep 22, 2018 |
| Title |
DLTPrc CvgrR-his |
| Sample type |
SRA |
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| Source name |
DLTPrc CvgrR-his
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| Organism |
Xanthomonas campestris pv. campestris str. 8004 |
| Characteristics |
genotype: prc mutant
treatment: osmostress
chip antibody: anti-His6 antibody (Abmart, #M20001, lot: 294073)
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| Treatment protocol |
The bacterial strains grown in NYG medium until OD600 = 0.8 ± 0.05 were treated with or without 800 mM sorbitol for 5 min.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
After collection by centrifugation, the samples were crossing-linked with 1% (V/V) formaldehyde for 20 min and subsequently quenched with 20% (V/V) 0.5 M glycine for 10 min. Then, the bacterial cells were recollected, washed with cold PBS (0.27 g/l KH2PO4, 1.42 g/l Na2HPO4, 8 g/l NaCl, and 0.2 g/l KCl, pH 7.4) twice, and resuspended in ChIP lysis buffer (10 mM Tris pH 8.0, 20% sucrose, 50 mM NaCl, 10 mM EDTA, pH 8.0, 10 mg/ml lysozyme, and 1 mM PMSF). Quadruple the lysis buffer volume of immuno-precipitation buffer (50 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS) was added to the bacterial cell suspension, and the suspension was sonicated with a Diagenode Bioruptor (Diagenode, Liège, Belgium), generating 100–300-bp DNA fragments.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
An Illumina HiSeq-2000 system (Illumina, San Diego, CA USA) was used for high-throughput sequencing, which was conducted by the Beijing Institute of Genomics genomic service.
The high-throughput sequencing reads were analysed using the Burrows–Wheeler Aligner method, and the cleaned reads were aligned to the genomic sequence database of X. campestris pv. campestris 8004.
Peak calling was conducted by MACS2
The consensus binding motif analysis was completed with MEME and FIMI tools in the MEME software suite.
Genome_build: GCA_000012105.1
Supplementary_files_format_and_content: wig files
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| Submission date |
Sep 21, 2018 |
| Last update date |
Sep 24, 2018 |
| Contact name |
ChaoYing Deng |
| E-mail(s) |
[email protected]
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| Phone |
+861064806152
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| Organization name |
Chinese Academy of Sciences
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| Street address |
No. 1 Beichen West Road, Chaoyang District
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| City |
BeiJing |
| State/province |
BeiJing |
| ZIP/Postal code |
100101 |
| Country |
China |
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| Platform ID |
GPL25598 |
| Series (1) |
| GSE120292 |
Chromatin immunoprecipitation sequencing of VgrR–DNA-binding landscapes |
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| Relations |
| BioSample |
SAMN10102208 |
| SRA |
SRX4726392 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3397751_DLTPrc_CvgrR-his_treat_afterfiting_NC_007086.1.wig.gz |
1.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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