Project description:E. coli RNA was hybridized to tiling arrays to study the pattern of gene expression across the chromosome. 1 sample for stationary phase and 1 for mid-exponential phase
Project description:We have deep sequenced the small transcriptome of Escherichia coli growing in LB and in MOPS, in exponential and stationary phase, and analyzed the resulting reads by a novel pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 14,000 small transcripts enriched during both growth stages. RNA samples were collected from total RNA pools or from crude ribosome pools and then size selected by electrophoresis to limit the products to 20-300nt.
Project description:We used trimethylpsoralen intercalation to map supercoiling across the E. coli chromosome. We treated E. coli cells with trimethylpsoralen and exposed them to UV light. Psoralen enters cells, intercalates between DNA base pairs, and crosslinks the two strands of DNA at a rate proportional to the local superhelical density. We then fragmented DNA and hybridized crosslinked and non-crosslinked DNA fragments separately to tiling microarrays.
Project description:To determine sites where RpoS binds (and hence likely plays a direct role in transcription), we used ChIP-seq to map the association of RpoS across the Escherichia coli chromosome during stationary phase growth in minimal medium. To facilitate ChIP, RpoS was C-terminally SPA-tagged at its native locus.
Project description:Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose E. coli rpoS deletion mutant grown up to OD600nm 1.5 (stationary phase) in M9 minimal media supplemented with 0.2% glucose. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide. Data for wild type controls are GSM389302, GSM389303, and GSM389304.
Project description:Differential expression of genes in E. coli MG1655 strains with deletions of fis and hns was assessed under early-exponential, mid-exponential, transition-to-stationary and stationary phases of growth in LB medium.
Project description:To compare the transcriptional profiling of a FimZ-expressing strain or non-expressing strain in E. coli under stationary phase. For overexpression of fimZ gene was cloned into pBAD33 plasmid under control of the arabinose-inducible PBAD promoter, which was induced by addition of 0.2% arabinose. Goal was to determine the FimZ regulon in E. coli. Biological replicates: 2 replicates.
Project description:The sensibility of the used low-density arrays was tested by applying the lab strain S. cerevisiae H155. Important abiotic parameters were tested as they were introduced as elevated osmotic, pH or ethanol stress to the cells.
Project description:Quorum signal uptake is an indispensable part of quorum sensing regulations. The coperative regulation of uptake repressor and kinase precisely signale the cells for quorum sensing uptake and terminate the quorum sensing signal production. We use the DNA microarray to detail the E. coli quorum sensing uptake reuglations and related gene regulations. Experiment Overall Design: W3110 wild type and its isogenic mutants lsrR, lsrK's RNA samples were extracted and hybridized for Affymetrix array.
Project description:The sensibility of the used low-density arrays was tested by applying the lab strain S. cerevisiae H155. Important abiotic parameters were tested as they were introduced as elevated osmotic, pH or ethanol stress to the cells. Results from one loop including samples from cells in five different conditions are summarized in this study. Microarrays were hybridized in a loop approach.