Project description:This ArrayExpress record contains meta-data and results of quantitative analysis of cell lines from the NCI-60 panel using pressure cycling technology (PCT) and SWATH-mass spectrometry. Each cell line was analyzed in duplicate. Raw data files are available at the EMBL-EBI protemics data archive (PRIDE) at accession PXD003539 (http://www.ebi.ac.uk/pride/archive/projects/PXD003539). Since the record here does not include the raw data files and hence there is no need to explicitly link individual replicate to a raw file, each sample is only listed once in the ArrayExpress samples table for clarity.
Project description:The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary intestinal stem cells. Applying quantitative mass spectrometry as well as transcriptomic analysis, we profiled the protein and gene changes between FACS-sorted Lgr5+ve stem cells and their immediate undifferentiated daughter cells. The overall comparison of mRNA and protein levels revealed a high level of correlation, implying that the initial control of intestinal stem cell biology occurs largely at the mRNA level. Taken together, our study presents a valuable resource for the study of intestinal stem cell biology. We used cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations, one expressing GFP at high levels (GFPhi) and the other expressing GFP at low levels (GFPlow). The gates set to sort cells for the expression profiling were the same as for the cells used for the mass spectrometry analysis. Differentially labelled cRNA from GFPhi and GFPlow cells from two different sorts (each combining three different mice) were hybridized on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F) in two dye swap experiments, resulting in four individual arrays.
Project description:Technological advances have enabled the analysis of cellular protein and RNA levels with unprecedented depth and sensitivity, allowing for an unbiased re?evaluation of gene regulation during fundamental biological processes. Here, we have chronicled the dynamics of protein and mRNA expression levels across a minimally perturbed cell cycle in human myeloid leukemia cells using centrifugal elutriation combined with mass spectrometry?based proteomics and RNA?Seq, avoiding artificial synchronization procedures.
Project description:The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary intestinal stem cells. Applying quantitative mass spectrometry as well as transcriptomic analysis, we profiled the protein and gene changes between FACS-sorted Lgr5+ve stem cells and their immediate undifferentiated daughter cells. The overall comparison of mRNA and protein levels revealed a high level of correlation, implying that the initial control of intestinal stem cell biology occurs largely at the mRNA level. Taken together, our study presents a valuable resource for the study of intestinal stem cell biology. We used cell fractions of intestines from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. RNA was isolated from two FACS sorted cell populations, one expressing GFP at high levels (GFPbright) and the other expressing GFP at low levels (GFPdim). The gates set to sort cells for the expression profiling were the same as for the cells used for the mass spectometry analysis. cRNA from GFPbright and GFPdim cells from three different sorts (each combining three to four mice) were hybridized on Affymetrix Mouse HT MG-430 PM plate arrays.
Project description:The investigation aims to profile the molecular dynamics of Rituximab treatment in cells. Specifically, primary B cells were treated with Rituximab, and sampled across 6 time points. Treated and untreated cells were processed to extract RNA and protein, that were subsequently used in high-throughput analysis of the transcriptome (RNA-Sequencing) and proteome (mass spectrometry).
Project description:Using mass spectrometry-based label-free quantitative (LFQ) proteomics analysis of in vitro differentiated murine Th17 and induced T regulatory (iTreg) cells. More than 4000 proteins covering almost all subcellular compartments were detected. Quantitative comparison of the protein expression profiles resulted in the identification of proteins specifically expressed in the Th17 and iTreg cells. Importantly, our combined analysis of proteome and gene expression data revealed protein expression changes that were not associated with changes at the transcriptional level.
Project description:Polycystic ovary syndrome (PCOS) is a common disorder encompassing reproductive, metabolic, and endocrine abnormalities, affecting 5 to 10% of women of reproductive age.To reveal the differences in proteomic profiles of follicular fluid between patients with and without PCOS and explore possible mechanisms underlying PCOS.Follicular fluid samples were collected from 9 infertile patients with PCOS and 9 infertile patients without PCOS. Quantitative proteomics analysis based on mass spectrometry was used to measure the protein levels and understand the protein networks. The tandem mass tag (TMT) based proteomics technology and bioinformatics analysis were used to determine the differentially expressed proteins(DEPs). : In this study, we have identified a total of 1216 proteins,these included 70 DEPs, in which 32 proteins were upregulated, and 38 proteins were downregulated. The bioinformatics analyses revealed multiple biological functions associated with these DEPs, some DEPs were enriched in the immune and metabolic-related biological processes in PCOS patients.
Project description:The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary intestinal stem cells. Applying quantitative mass spectrometry as well as transcriptomic analysis, we profiled the protein and gene changes between FACS-sorted Lgr5+ve stem cells and their immediate undifferentiated daughter cells. The overall comparison of mRNA and protein levels revealed a high level of correlation, implying that the initial control of intestinal stem cell biology occurs largely at the mRNA level. Taken together, our study presents a valuable resource for the study of intestinal stem cell biology.
Project description:The identification of Lgr5 as an intestinal stem cell marker has made it possible to isolate and study primary intestinal stem cells. Applying quantitative mass spectrometry as well as transcriptomic analysis, we profiled the protein and gene changes between FACS-sorted Lgr5+ve stem cells and their immediate undifferentiated daughter cells. The overall comparison of mRNA and protein levels revealed a high level of correlation, implying that the initial control of intestinal stem cell biology occurs largely at the mRNA level. Taken together, our study presents a valuable resource for the study of intestinal stem cell biology.