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| Status |
Public on Aug 04, 2015 |
| Title |
soxR1 |
| Sample type |
SRA |
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| Source name |
liquid culture in LB
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| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: MPAO1/pAK1900-soxR-vsv
chip antibody: anti-VSV
technology: ChIP-seq
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| Treatment protocol |
grow until mid-log phase
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| Growth protocol |
LB medium with Amp
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Wild type P. aeruginosa MAPO1 containing empty pAK1900 or pAK1900-VqsM-VSV was cultured in LB medium supplemented with ampicillin until the mid-log phase (OD=0.6), before was treated with 1% formaldehyde for 10 min at 37 °C. Cross-linking was stopped by addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl), and then re-suspended in 500 µl IP buffer (50 mM Hepes-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail (Roche) and sonicated the DNA to sizes of 100-300 bp. Insoluble cellular debris was removed by centrifugation and the supernatant used as input sample in IP experiments. Both control and IP samples were washed by protein A beads (General Electric), and then incubated with 50 ul agarose-conjugated anti-VSV antibodies (Sigma) in IP buffer. Washing, crosslink reversal, and purification of the ChIP DNA were conducted by following previously published protocols.
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
soxrvsvmacs2_peaks.xls
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| Data processing |
Bacterial ChIP-seq reads were mapped to the P. auruginosa genome (ASM676v1), using TopHat (version 2.0.0) with two mismatches allowed.
Only the uniquely mapped reads were kept for the subsequent analyses.
The enriched peaks were identified using MACS software (version 2.0.0)
Genome_build: P. aeruginosa PAO1 (ASM676v1)
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| Submission date |
Jan 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xin Deng |
| E-mail(s) |
xindeng@cityu.edu.hk
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| Phone |
852-34425693
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| Organization name |
City University of Hong Kong
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| Department |
Biomedical Sciences
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| Street address |
To Yuen Building
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| City |
Hong Kong |
| ZIP/Postal code |
60637 |
| Country |
Hong Kong |
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| Platform ID |
GPL18644 |
| Series (2) |
| GSE65356 |
ChIP-seq analyses of 10 quorum sensing regulators in Pseudomonas aeruginosa |
| GSE110522 |
RpoN-dependent global regulation in Pseudomonas aeruginosa PAO1 |
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| Relations |
| BioSample |
SAMN03295689 |
| SRA |
SRX856372 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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