Project description:Here as an attempt to explore bacterial single-colony proteomics, we describe a quantitative mass spectrometry-based protocol to isolate and analyse the proteome of a single mycobacterial colony from 7H10 media. Tryptic peptides are evaluated with high performance liquid chromatography coupled with a hybrid quadrupole mass filter Orbitrap analyser (Q Exactive) and raw data analysed using the MaxQuant Suite and downstream analysis using Perseus software . A total of 7805 unique peptides and 1387 proteins were identified
Project description:Metaproteomes of individual Trichodesmium colonies collected from a single location in the Carribbean sea (65.22W, 17.02N) at 17:00 local time. Some colonies were associated with auto-fluorescent mineral particles. Their proteomes were analyzed individually to investigate the effect of the minerals on colony physiology.
Project description:Purpose: Assess the cellular heterogeneity during the transition through partial EMT and MET in the spontaneous C3(1)-Tag breast cancer model. Methods: We performed MULTI-seq single cell RNA sequencing analysis in two different ex vivo assays: the collagen assay that models invasion and the colony formation assay that models metastatic outgrowth. Briefly, organoids were isolated from 4 different mice and either plated directly into collagen I matrix or further dissociated into clusters and plated into Matrigel. Cells were removed from the matrix and dissociated into single cells at day 0 (12h in matrix), day 3 and day 5. For each day, cells were barcoded by mouse and matrix and flow sorted for live cells before being processed on the 10X Genomics platform for barcoding and library construction. As a control for batch effect during library construction for the different time point, we added a cell line control (4T1) at each day. Finally, the libraries were sequenced together using the NOVAseq. Results: We sequenced 8,908 cells. After correction for batch effect, we performed a pseudotime analysis. We observed a temporal progression of the cells during invasion and colony formation. This transition is associated with a decrease in E-cadherin and an increase in vimentin expressions as well as other EMT genes during invasion and the opposite during colony formation. These results demonstrated at the single cell resolution that there is a temporal progression associated with EMT and MET during invasion and colony formation, respectively.
Project description:Most of the proteomic studies done so far uses bacterial cells harvested from liquid culture media. However it is widely accepted that many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth on solid media. As an attempt to complement previous studies, in this study we compare the proteome coverage of Escherichia coli K12 from a single colony on solid media with those at different growth phases in liquid culture; i.e. early log, mid log, early - and late stationary growth phases. A total of 2044 protein groups covering approximately 47% of the total proteome were identified across all studied conditions; 1650 number of proteins identified from single colonies and 1679 proteins from liquid cultured cells. Label-free quantitative analysis revealed that single colony proteome in a solid agar differs largely from that in liquid culture. The presence of the Suf-operon, involved in iron mobilisation and swarming motility were associated exclusively with single colony profiles. Whereas proteins involved in motility such as MotA, MotB, fliH, flip, fliD and fliJ were associated exclusively to cells grown in liquid culture. The data presented here provide a valuable resource for understanding the role of key proteins within microenvironments surrounding E.coli single colonies.
Project description:We performed high throughput RNA-sequencing on KSHV-infected blood and lymphatic Endothelial Colony-Forming Cells at 48hpi to identify differences in gene expression induced by KSHV in these two cell types.
Project description:We selected humann intervertebral disc samples to perform proteomics analysis. There were 1 case of grade I , 1 case of grade II, 3 cases of grade Ⅲ and 3 cases of grade Ⅳ according to Pfirrmann classfication. RNA seqencing analysis and single-cell RNA sequencing were integrated with proteomics data to identify the hub genes for intervertebral disc degeneration using bioinformatic method.
