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ABSTRACT: EHEC Sakai O157:H7 tolerance to the antimicrobial flexicate Λ-5b

PROVIDER: PRJNA517036 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8486190_1.fastq.gz	Fastqsanger.gz
	SRR8486190_2.fastq.gz	Fastqsanger.gz
	SRR8486191_1.fastq.gz	Fastqsanger.gz
	SRR8486191_2.fastq.gz	Fastqsanger.gz
	SRR8486182_1.fastq.gz	Fastqsanger.gz

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RNAseq of E. coli Sakai O157:H7 in the presence of the flexicate compound Λ-5b

Project description:The synthetic flexicate compound Λ-5b shows potent antimicrobial activity against E. coli. In this study we investigated the transcriptomic response of a clinically relevant E. coli, EHEC O157:H7, to a sublethal concentration of the compound.

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EHEC O157:H7 Sakai vs. TW14359: Secreted and Cytosolic iTRAQ; sepD secretome analysis of TW14359

Project description:Comparative analysis of EHEC O157:H7 Sakai vs. TW14359 secreted and cytosolic protein using iTRAQ and mass spectrometry on an LTQ Orbitrap. Samples were fractionated through strong cation exchange and HPLC before analsyis. For TW14359 sepD secretome analysis, strains were similarly prepared and analyzed. All samples were searched against a TW14359 specific protein database (Uniprot) coupled with randomized protein sequences.

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2D-LC/MS/MS analysis of Escherichia coli under optimal growth condition

Project description:2D-LC/MS/MS analysis was used to examine the proteome of E. coli O157:H7 strain Sakai during exponential growth under optimal condition (i.e., from 35°C aw 0.993). MS/MS data obtained from each protein sample were processed by the Computational Proteomics Analysis System (CPAS), a web-based system built on the LabKey Server (v9.1, released 02.04.2009). The experimental mass spectra produced were subjected to a semi-tryptic search against the combined databases of E. coli O157:H7 Sakai (5,318 entries in total) downloaded from the National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/, downloaded 25.11.2008) using X!Tandem v2007.07.01. These databases included the E. coli O157:H7 Sakai database (5230 entries, NC_002695.fasta) and two E. coli O157:H7 Sakai plasmid databases, plasmid pO157 (85 entries, NC_002128.fasta) and plasmid pOSAK1 (three entries, NC_002127.fasta). The parameters for the database search were as follows: mass tolerance for precursor and fragment ions: 10 ppm and 0.5 Da, respectively; fixed modification: cysteine cabamidomethylation (+57 Da); and no variable modifications. The search results were then analyzed using the PeptideProphet and ProteinProphet algorithms from the Trans Proteomic Pipeline v3.4.2. All peptide and protein identifications were accepted at PeptideProphet and ProteinProphet of ≥0.9, corresponding to a theoretical error rate of ≤2%.

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2D-LC/MS/MS analysis of Escherichia coli during exposure to an abrupt temperature downshift

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RNAseq of E. coli Sakai O157:H7 in the presence of the flexicate compound Λ-5b

Project description:RNAseq of E. coli Sakai O157:H7 in the presence of the flexicate compound Λ-5b

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Chromatin immunoprecipitation of Escherichia coli HNS-FLAG pchABC, pchBC and Ler mutants to determine Pch and H-NS distribution

Project description:Pch and H-NS distribution in EHEC O157 Sakai

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Escherichia coli strain:O157:H7 Sakai (EHEC)

Project description:Escherichia coli strain:O157:H7 Sakai (EHEC) Raw sequence reads

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