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Sample GSM1593062 Query DataSets for GSM1593062
Status Public on Aug 04, 2015
Title wspR2
Sample type SRA
 
Source name liquid culture in LB
Organism Pseudomonas aeruginosa
Characteristics strain: MPAO1/pAK1900-wspR-vsv
chip antibody: anti-VSV
technology: ChIP-seq
Treatment protocol grow until mid-log phase
Growth protocol LB medium with Amp
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)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description wsprvsvmacs2e4_peaks.xls
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)
 
Submission date Jan 27, 2015
Last update date May 15, 2019
Contact name Xin Deng
E-mail(s) xindeng@cityu.edu.hk
Phone 852-34425693
Organization name City University of Hong Kong
Department Biomedical Sciences
Street address To Yuen Building
City Hong Kong
ZIP/Postal code 60637
Country Hong Kong
 
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
Relations
BioSample SAMN03295701
SRA SRX856389

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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