Project description:Nowadays, although single-cell multi-omics technologies are undergoing rapid development, simultaneous transcriptome and proteome analysis of a single-cell individual still faces great challenges. Here, we developed a single-cell simultaneous transcriptome and proteome (scSTAP) analysis platform based on microfluidics, high-throughput sequencing and mass spectrometry technology, to achieve deep and joint quantitative analysis of transcriptome and proteome at the single-cell level, providing an important resource for understanding the relationship between transcription and translation in cells. This platform was applied to analyze single mouse oocytes at different meiotic maturation stages, reaching an average quantification depth of 19948 genes and 2663 protein groups in single mouse oocytes.
Project description:Inhibitors of glucose (IO+DHEA group) or fatty acids (ETOMOXIR group) metabolism were applied during bovine oocyte in vitro maturation (IVM). Control group was conducted in standard maturation conditions. In vitro fertilization and embryo culture were applied. Obtained blastocysts were analysed with regard to lipidome, metabolome (mass spectrometry), transcriptome (RNA Seq) and lipid droplets staining (BODIPY).
Project description:The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides was lacking. To this end, Akhilesh Pandey's lab reported a draft map of the human proteome based on high resolution Fourier transform mass spectrometry-based proteomics technology, which included an in-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells ( http://dx.doi.org/10.1038/nature13302 ). The profiling resulted in identification of proteins encoded by greater than 17,000 genes accounting for ~84% of the total annotated protein-coding genes in humans. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) complements available human genome and transcriptome data to accelerate biomedical research in health and disease. Pandey's lab and collaborators request that those considering use of this primary dataset for commercial purposes contact pandey@jhmi.edu. The full details of this study can be found in the PRIDE database: www.ebi.ac.uk/pride/archive/projects/PXD000561/. This ArrayExpress entry represents a top level summary of the metadata only which formed the basis of the reanalysis performed by Joyti Choudhary's team ( jc4@sanger.ac.uk ), results of which are presented in the Expression Atlas at EMBL-EBI : http://www.ebi.ac.uk/gxa/experiments/E-PROT-1.
Project description:RNA-seq experiments measuring global RNA abundance Temperature sensitive (TS) mutants are a tool that have been foundational for the study of many essential life processes. Despite the long-term use of TS mutants, the mechanisms that lead to temperature sensitivity are not fully understood. Furthermore, a high-throughput workflow to characterize biophysical changes occurring in TS mutants is lacking. We developed Temperature sensitive Mutant Proteome Profiling (TeMPP), a novel application of mass spectrometry based thermal proteome profiling (TPP) as a way to measure the effects of missense mutations on protein stability and protein-protein interactions. This study characterized the global changes in mRNA abundance, protein abundance, and protein thermal stability as a result of missense mutants within two subunits of the yeast ubiquitin-proteasome system. Global protein abundance measurements and RNA sequencing data resulted in a large number of possible candidates that could be causing the phenotypic changes observed in the mutant strains. The additional information gained from TeMPP along with complementary proteomic and transcriptomic experiments allows for multiomic intersection analysis that may reveal interesting regulatory categories to pursue in follow-up mechanistic experiments.
Project description:Defining the subcellular distribution of all human proteins and its remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immuno-capture coupled to mass spectrometry. We apply this workflow to a cell-wide collection of membranous and membrane-less compartments. A graph-based analysis reveals the subcellular localization of over 7,600 proteins, defines spatial networks, and uncovers interconnections between cellular compartments. Our approach can be deployed to comprehensively profile proteome remodeling during cellular perturbation. By characterizing the cellular landscape following hCoV-OC43 viral infection, we discover that many proteins are regulated by changes in their spatial distribution rather than by changes in abundance. Our results establish that proteome-wide analysis of subcellular remodeling provides unique insights for the elucidation of cellular responses, uncovering an essential role for ferroptosis in OC43 infection. Our dataset can be explored at organelles.czbiohub.org.
Project description:Proteome-level data of non-small cell lung cancer remains limited. In this study, we have collected 141 cases, and performed histological review, methylation profiling (113), custom panel sequencing (140), microarray expression profiling (118) and mass-spectrometry based proteomics (141). We identified six distinct groups of patients driven by histology, growth pattern, immune cell infiltration, druggable driver mutations, and hypomethylation-associated neoantigen burden. We validated the subtypes in independent proteomics datasets. Proteomics can refine treatment-oriented subtyping of non-small cell lung cancer.
Project description:We present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii.
Project description:Numerous genes mutated in amyotrophic lateral sclerosis (ALS) share a role in DNA damage and repair, emphasizing genome disintegration in ALS. DNA instability and repair mechanisms segregate extrachromosomal circular DNAs (ec/eccDNAs) that can modulate gene expression somatically. Here, circulome profiling in a hSOD1G93A genotoxicity model of ALS revealed a 6-fold enrichment of small-size eccDNAs relative to controls. DifCir-based differential analysis identified 189 genes with patterned segregation of differentially produced per gene circles (DPpGCs) from ALS but not from control samples, implicating an inter-sample recurrence rate of at least 89% for the top 6 DPpGCs. Mass spectrometry-based ALS circulome-proteome cross-referencing revealed 31 corresponding differentially expressed proteins (DEPs), with 12 DPpGC-DEP pairs being itemized in ALS risk GWAS databases. DPpGC-DEP hotspots mainly convey neuron-specific functions counteracting ALS detriments. This is unanticipated evidence for non-random, profiled eccDNA accumulation in ALS neurodegeneration, involving putative interactions with their gene products as well as biomarker perspectives.