Project description:Expression data comparing typical E.coli colonies grown on BHI and BHI+Sucrose+MgSO4 to L-form colonies grown on BHI+Sucrose+MgSO4+Penicillin G. Keywords: one time point
Project description:Expression data comparing typical E.coli colonies grown on BHI and BHI+Sucrose+MgSO4 to L-form colonies grown on BHI+Sucrose+MgSO4+Penicillin G. Keywords: one time point DNA microarray analysis of E.coli colonies grown on BHI and BHI+Sucrose+MgSO4 (controls) with L-form colonies grown on BHI+Sucrose+MgSO4+Penicillin G (experimental). An isolated colony of fresh W3110 was grown for 5hrs to log phase, dilutions of the inoculmn were spread onto three media: BHI, BHI+Sucrose+MgSO4, and BHI+Sucrose+MgSO4+Penicillin G to yield isolated colonies. Isolated control colonies which grow overnight were harvested the next day while isolated L-form colonies which do not grow until 48-72 hrs were harvested after 72hrs. All colonies were harvest with a PBS moistened sterile swab and dipped into a sterile microcentrifuge tube containing 500ul of PBS. RNA was isolated from pelleted cells using MasterPure RNA Purification Kit and reverse transcribed for making probes for array hybridization on E.coli Genome 2.0 Affymetrix microarrays.
Project description:We report RNA sequencing data for mRNA transcripts obtained from tobramycin exposed phoenix colonies, VBNCs, and various controls (untreated lawn, edge of the zone of clearance of tobramycin, treated outer background lawn). Extracted mRNA was sequenced using an Illumina HiSeq 4000, mapped to a Pseudomonas aeruginosa PAO1 reference genome, and processed to obtain counts for all gene transcripts for each sample. This is the first sequencing data generated for Pseudomonas aeruginosa phoenix colonies and VBNCs.
Project description:We report the development and application of isogenic colony sequencing to profile heterogeneity among yeast colonies. We profiled transcriptomes of the opaque-white switching in C. albicans colonies and an ARO4 mutagenesis library in S. cerevisiae colonies.
Project description:Saccharomyces cerevisiae colonies were grown for 2 days on synthetic minimal media with 1% glucose, with and without 400uM lysine (5 colonies/biological replicates each). Whole colonies were then used for proteome profiling by SWATH-MS for differential gene expression analysis. A number of genes were identified that respond to lysine supplementation, most notably genes involved in lysine biosynthesis.
Project description:Human multipotent stromal cells readily form single-cell-derived colonies when plated at clonal densities. However, the colonies are heterogeneous because cells from a colony form new colonies that vary in size and differentiation potential when replated at clonal densities. The experiments here tested the hypothesis that cells in the inner regions of colonies are partially differentiated, but the differentiation is reversible. Cells were separately isolated from the dense inner (IN) regions and less-dense outer regions (OUT) of single-cell-derived colonies. Cells were then compared by assays of their transcriptomes and proteins, and for clonogenicity and differentiation. IN cells expressed fewer cell-cycle genes and higher levels of genes for extracellular matrix than the OUT cells. When transferred to differentiation medium, differentiation of the colonies occurred primarily in the IN regions. However, the IN cells were indistinguishable from OUT cells when replated at clonal densities and assayed for rates of propagation and clonogenicity. Also, colonies formed by IN cells were similar to colonies formed by OUT cells because they had distinct IN and OUT regions. Cultures of IN and OUT cells remained indistinguishable through multiple passages (30-75 population doublings), and both cells formed colonies that were looser and less dense as they were expanded. The results demonstrated that cells in the IN region of single-cell-derived colonies are partially differentiated, but the differentiation can be reversed by replating the cells at clonal densities.
Project description:RNA-Sequencing performed on 177 honey bee whole-brains, divided into "soldier" and "forager" groups from Puerto Rican honey bee colonies.
