Project description:PTex is a protocol to purify UV-cross-linked ribonucleoproteins (RNPs) in an unbiased and sequence-independent fashion. Total RNA from HEK293 cells was analysed by RNASeq from whole cell lysates as well as after purification of RNPs.
Project description:Recent advancements in neuroproteomics have enabled detailed analysis of protein expression and function in the human brain, improving our understanding of the relationship between genetics, cell biology of neurological and psychiatric disorders and their clinical diagnosis. Synaptic dysfunction often has a central role in these disorders. Leveraging the high sensitivity of modern liquid chromatography-tandem mass spectrometry (LC-MS/MS), we here evaluated the detection of synaptic proteins in whole-tissue lysates compared to enriched synaptosome preparations. First, we optimized sample preparation protocols for frozen human gray matter (GM), refining the suspension TRAPping (sTRAP) digestion method to improve protein solubilization and Cysteine reduction and alkylation using thin human tissue sections, and to accomplish low technical variation by minimizing sample handling. We achieved a highly reproducible sample preparation workflow by rigorously applying standardization and randomization across dissection, processing, and LC-MS/MS runs. Second, comparative LC-MS/MS analysis showed that cortical whole-tissue lysates are a practical solution for large-scale studies and broadly detected synaptic proteins. However, synaptosome isolation offered improved resolution of synapse-specific proteins. Because synapse-proteomics enables insight into spatial regulation—i.e., alterations at the synapse not reflected in the soma– we recommend a tiered approach for large-scale studies: initial whole-tissue lysate analysis for broad disease-associated changes, followed by targeted synaptosome proteomics to deepen insight into synaptic alterations. This strategy optimally balances throughput, reproducibility, and biological relevance, and enhances the study of brain disorders through proteomics. Moreover, analyzing synaptic proteins first at the tissue level improves insight into overall regulation of synaptic proteins induced by synapse loss or gain.
Project description:We performed proteomic analysis of extracellular vesicles (EVs) and whole cell lysates (WCL) isolated from the same biofilm (strain = DAY286, n = 5). We identified proteins enriched in EVs versus WCL by comparing their LFQ intensities across all samples. After linking these results with EV enrichment data from other strains, we proposed a suite of putative EV marker proteins which were useful for multiple C. albicans strains and morphologies.
Project description:The “Pan-Human Library” is a compendium of highly specific assays covering more than 10 000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This dataset contains validation SWATH-MS data and OpenSWATH results of whole cell lysates of HeLa (guot_L130330_005_SW, guot_L130330_006_SW, guot_L130330_007_SW) and U2OS cells (gout_L130330_013_SW, gout_L130330_014_SW, gout_L130330_015_SW). Further, the combined assay library (phl004_s32.csv) and the sample-specific assay libraries (phl004_sshela_s32.csv, phl004_ssu2os.csv) used for the analysis are provided.
Project description:We performed proteomic analysis of extracellular vesicles (EVs) and whole cell lysates (WCL) isolated from the same liquid culture (strain = DAY286, n = 3). This data set is the first label-free quantitative comparative study of the proteins in C. albicans EVs and their parent planktonic (yeast-form) cells. We identified proteins enriched in EVs versus WCL by comparing their LFQ intensities across all samples. After linking these results with EV enrichment data from other strains, we proposed a suite of putative EV marker proteins which were useful for multiple C. albicans strains and morphologies.
Project description:To explore the role of circRNAs during CRC (colorectal cancer) metastasis, we isolated CRC cells from human sample and performed transwell assay. Then circRNA microArray analysis were performed and differentially expressed circRNAs were identified.
Project description:The aim of this study was to provide proof of principle as to whether probiotic bacteria or their extracts, could stimulate cutaneous wound healing. To this end, we have used a keratinocyte monolayer scratch assay which assesses one important aspect of wound healing, re-epithelialization. Primary human keratinocyte monolayers were scratched and then exposed to lysates of Lactobacillus rhamnosus GG
Project description:The long term goal is to define the transcriptional changes that accompany pericyte-to-myofibroblast transition in fibrotic kidney disease. Medullary pericytes are identified by their expression of a eGFPL10a fusion protein whose expression is driven by a Col1a1 promoter. Pericyte-specific RNA is generated by eGFP-affinity purification of polysomes from medullary lysates and then subject to microarray analysis.
Project description:We performed proteomic analysis of extracellular vesicles (EVs) and whole cell lysates (WCL) isolated from the same liquid culture. This was implemented for two different C. albicans strains, ATCC90028 (n = 3) and ATCC10231 (n = 3). This data set is the first label-free quantitative comparative study of the proteins in C. albicans EVs and their parent planktonic (yeast-form) cells. We identified proteins enriched in EVs versus WCL by comparing their LFQ intensities across all samples. After linking these results with EV enrichment data from other strains, we proposed a suite of putative EV marker proteins which were useful for multiple C. albicans strains and morphologies.
Project description:Commercial human heart whole tissue lysates were analyzed with LC-MS/MS with an inclusion list of alternative sequences (Lau et al. bioRxiv 2019).