Browse
Submit Data
Databases
API
Help

Dataset Information

349 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CEGS Proteomics - A multiregional proteomic survey of the postnatal human brain

ABSTRACT: Here we exploit label-free quantitative tandem mass-spectrometry proteomics to create the first in-depth quantitative proteomic survey of regions of the postnatal human brain. We adopted a dual approach to analysing these human brain samples similar to that of a recent high-quality study of the mouse brain proteome by Sharma et al, 2015. First was the discovery phase, designed to create a highly sensitive, heavily fractionated spectral library for each adult brain region. Then, to produce a quantitative run for each adult and postnatal development sample, single shot LC-MS/MS runs were used to accurately quantify proteins based on detected precursor peptide ion mass.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Brain

SUBMITTER: TuKiet Lam

LAB HEAD: TuKiet T. Lam

PROVIDER: PXD005445 | Pride | 2018-01-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MaxQuant_Output.zip	Other
	QEp15-2550_CON.raw	Raw
	QEp15-2554_AMY.raw	Raw
	QEp15-2558_AMY.raw	Raw
	QEp15-2562_AMY.raw	Raw

Items per page:

1 - 5 of 199

Publications

A multiregional proteomic survey of the postnatal human brain.

Carlyle Becky C BC Kitchen Robert R RR Kanyo Jean E JE Voss Edward Z EZ Pletikos Mihovil M Sousa André M M AMM Lam TuKiet T TT Gerstein Mark B MB Sestan Nenad N Nairn Angus C AC

Nature neuroscience 20171113 12

Detailed observations of transcriptional, translational and post-translational events in the human brain are essential to improving our understanding of its development, function and vulnerability to disease. Here, we exploited label-free quantitative tandem mass-spectrometry to create an in-depth proteomic survey of regions of the postnatal human brain, ranging in age from early infancy to adulthood. Integration of protein data with existing matched whole-transcriptome sequencing (RNA-seq) from ...[more]

PMID: 29184206

Similar Datasets

Proteomic Characterization of Post-Mortem Human Brain Tissue Following Ultracentrifugation-based Subcellular Fractionation

Project description:Proteomic characterization of human brain tissue is increasingly utilized to identify potential novel biomarker and drug targets for a variety of neurological diseases. In whole tissue studies, results may be driven by changes in the proportion of the largest and most abundant organelles or tissue cell-type composition. Spatial proteomics approaches enhance our knowledge of disease mechanisms and changing signaling pathways at the subcellular level by taking into account the importance of cellular localization, which critically influences protein function. Density gradient-based ultracentrifugation methods allow for subcellular fractionation and have been utilized in cell lines and fresh mouse brain tissue to predict the subcellular location of thousands of proteins, but to our knowledge have not been used in frozen human brain tissue. The use of frozen human tissue for tissue fractionation faces two major challenges, the post-mortem interval, during which proteins may leach from their usual location into the cytosol, and freezing, which results in membrane breakdown. Despite these challenges, in this proof-of-concept study, we show that the majority of proteins segregate reproducibly into crude density-based centrifugation fractions, that the fractions are enriched for the appropriate organellar markers, and that significant differences in protein localization can be observed between tissue from individuals with Alzheimer’s Disease and control individuals.

2022-05-06 | PXD027456 | Pride

Caveat Mutator

Project description:The use of whole genome microarrays for monitoring mutagenised or otherwise engineered genetic derivatives is a potentially powerful tool for checking genomic integrity. Using comparative genomic hybridization of a number of unrelated, directed deletion mutants in Escherichia coli K-12 MG1655 we identified unintended secondary genomic deletions in the flhDC region in fnr, crp, and creB mutants. These deletions were confirmed by PCR and phenotypic tests. Our findings show that non-motile progeny are found in some populations of MG1655 directed deletion mutants, and studies on the effects of gene knock-outs should be viewed with caution when the mutants have not been screened for the presence of secondary deletions, or confirmed by other methods. We used the CGH method to genetically characterize a series of regulatory gene deletion mutants we had made in MG1655 using the lamda-Red method of Datsenko and Wanner. A number of strains were tested using CGH, and each strain was tested only once. Genomic DNA isolated from wt MG1655 was used as a reference in all hybridisations.

2007-09-30 | E-GEOD-7695 | biostudies-arrayexpress

Deep proteomic analysis of human microglia and model systems reveal fundamental biological differences of in vitro and ex vivo cells - mouse validation data set

Project description:Using high resolution quantitative mass spectrometry, we have generated the most comprehensive human and mouse microglia proteomic datasets to date, consisting of over 11,000 proteins across all six microglia groups. Microglia from different sources share a core protein signature of over 5600 proteins, yet fundamental differences are observed between species and culture conditions, indicating limitations for human disease modelling in mouse or in in vitro cultures of microglia. Mouse ex vivo microglia show important differences at the proteome level such as differential expression of inflammation and Alzheimer’s Disease associated proteins. We identify a tenfold difference in protein content of ex vivo and in vitro cells and significant proteome differences associated with protein synthesis, metabolism, microglia marker expression and environmental sensors. Culturing microglia induces rapidly increased growth, protein content and inflammatory protein expression. These changes can be restored by engrafting in vitro cells into the brain, with xenografted hESC-derived microglia closely resembling microglia from human brain. This data provides an important resource for the field and highlights important considerations needed when using model systems to study human physiology and pathology of microglia.

2024-10-23 | PXD056488 | Pride

Capillary zone electrophoresis-tandem mass spectrometry for top-down proteomics of mouse brain integral membrane proteins

Project description:Mass spectrometry (MS)-based top-down characterization of integral membrane proteins (IMPs) is crucial for understanding their functions in biological processes. However, it is technically challenging due to their low solubility in typical MS-compatible buffers. In this work, for the first time, we developed an efficient capillary zone electrophoresis (CZE)-tandem MS (MS/MS) method for top-down proteomics (TDP) of IMPs enriched from mouse brains. Our technique employs a sample buffer containing 30% (v/v) formic acid and 60% (v/v) methanol for solubilizing IMPs and utilizes a separation buffer of 30% (v/v) acetic acid and 30% (v/v) methanol for maintaining the solubility of IMPs during CZE separation. Single-shot CZE-MS/MS identified 51 IMP proteoforms from the mouse brain sample. Coupling size exclusion chromatography (SEC) to CZE-MS/MS enabled the identification of 276 IMP proteoforms from the mouse brain sample and those proteoforms contained 1-4 transmembrane domains. This proof-of-concept work demonstrates the high potential of CZE-MS/MS for large-scale TDP of IMPs.

2023-12-07 | PXD042298 | Pride

Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia.

Project description:Background: Schizophrenia is a severe neuropsychiatric disorder that is hypothesized to result from disturbances in early brain development, and there is mounting evidence to support a role for developmentally-regulated epigenetic variation in the molecular etiology of the disorder. Here, we describe a systematic study of schizophrenia-associated methylomic variation in the adult brain and its relationship to changes in DNA methylation across human fetal brain development. Results: We profile methylomic variation in matched prefrontal cortex and cerebellum brain tissue from schizophrenia patients and controls, identifying disease-associated differential DNA methylation at multiple loci, particularly in the prefrontal cortex, and confirming these differences in an independent set of adult brain samples. Our data reveal discrete modules of co-methylated loci associated with schizophrenia that are enriched for genes involved in neurodevelopmental processes and include loci implicated by genetic studies of the disorder. Methylomic data from human fetal cortex samples, spanning 23 to 184 days post-conception, indicates that disease-associated differentially methylated positions are significantly enriched for loci at which DNA methylation is dynamically altered during human fetal brain development. Conclusions: Our data support the hypothesis that schizophrenia has an important early neurodevelopmental component, and suggest that epigenetic mechanisms may mediate these effects. 33 post-mortem brain (prefrontal cortex) samples (18 schizophrenia cases and 15 controls) were obtained from Douglas Bell-Canada Brain Bank (DBCBB), Montreal, Canada. Bisulfite converted DNA from these samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.0.

2014-09-13 | E-GEOD-61380 | biostudies-arrayexpress

EMpire: Deep isoform level integration of the transcriptome, translatome, and proteome

Project description:In this study, we make used of mRNA-seq and its ability to reliably quantify isoforms, integrating this data with ribosome profiling and LC-MS/MS, to assign ribosome footprints and peptides at the isoform level. We leverage the principle that most cell types, and even tissues, predominantly express a single principal isoform to set isoform-level mRNA-seq quantifications as priors to guide and improve allocation of footprints or peptides to isoforms. Through tightly integrated mRNAseq, ribosome footprinting and/or LC-MS/MS proteomics we demonstrate that a principal isoform can be identified in over 80% of gene products in homogenous HEK293 cell culture and over 70% of proteins detected in complex human brain tissue. Defining isoforms in experiments with matched RNA-seq and translatomic/proteomic data increases the functional relevance of such datasets and will further broaden our understanding of multi-level control of gene expression. In this PRIDE submission you will find the raw files for the HEK293 cell proteomics. Files for the human brain proteomics can be found at PXD005445. We have also uploaded a zip file that contains the input files for our HEK293 cell analysis, and the isoform level output files – there is a separate folder within the zip files for these. The data used to create the manuscript figures is in the Rdata file. Code for assigning peptides and footprints to isoforms can be found on Github here: https://github.com/rkitchen/EMpire

2018-08-21 | PXD008693 | Pride

Proteome Profiling in Cerebrospinal Fluid Reveals Novel Biomarkers of Alzheimerâ€™s Disease

Project description:Neurodegenerative diseases are a growing burden and there is an urgent need for better biomarkers for diagnosis, prognosis and treatment efficacy. Structural and functional brain alterations are reflected in the protein composition of cerebrospinal fluid (CSF). Alzheimerâ€™s disease (AD) patients have higher CSF levels of tau, but we lack knowledge of systems-wide changes of CSF protein levels that accompany AD. Here we present a highly reproducible mass spectrometry (MS)-based proteomics workflow for the in-depth analysis of CSF from minimal sample amounts. From three independent studies (>200 individuals), we characterize differences in proteins by AD status (>1,000 proteins, CV<20%). Proteins with previous links to neurodegeneration such as tau, SOD1 and PARK7 differed most strongly by AD status, providing strong positive controls for our approach. CSF proteome changes in Alzheimerâ€™s disease prove to be widespread and often correlated with tau concentrations. Our unbiased screen also reveals a consistent glycolytic signature across our and a recent report (bioRxiv.org doi.org/10.1101/806752). Successful reclassification of individual patients and a machine learning model suggests clinical utility of our proteomic signature.

2020-05-26 | PXD016278 | Pride

the proteomic data of systematic organs of CHIKV-infected mouse and rhesus monkey

Project description:this proteomic data is compromised of 72 samples from 6 mouses and 6 rhesus monkeys. CHIKV, as a mosquito-based virus, is well known to pose threat to muscles and joints, with its symptoms being called chikunkunya fever, whereas its impact on other organs after infection is not completely understood. So we attempt to investigate whether it will cause damage to other organs with infected heart, liver, spleen, lung, kidney, and brain being study object.

2024-05-31 | PXD048726 | Pride

Long-term nutritional regulation of liver proteome

Project description:Nutrient sensing pathways influence metabolic health and aging, offering the possibility that diet might be used therapeutically, alone or with drugs targeting these pathways. We used the Geometric Framework for Nutrition to study interactive and comparative effects of diet and drugs on the hepatic proteome in mice across 40 dietary treatments differing in macronutrient ratios, energy density, and drug treatment (metformin, rapamycin, resveratrol).

2021-12-13 | PXD028928 | Pride

RNA-sequencing based analysis of Listeria monocytogenes 10403S::ÎBCHL Prha-sigH and ÎBCHL Prha

Project description:In this study, RNA-seq was used to compare the transcriptomes of Listeria monocytogenes 10403S::ÎBCHL Prha-sigH and ÎBCHL Prha. RNA-seq was performed on ÎBCHL Prha-sigH and ÎBCHL Prha RNA samples representing three independent biological replicates at log phase in Brain Heart Infusion (BHI) broth under rhamnose induction. Indexed and purified cDNA libraries (6 libraries including 3 replicates for 2 strains) were loaded together onto an independent flow cell without any other samples; sequencing was carried out by running Hiseq 2500 (single-end, 150-bp per read). Reads alignment was carried out using the Burrows-Wheeler Aligner (BWA). Differential expression of genes in different strains was statistically assessed using the BaySeq method. To identify sigH-dependent promoters, a new method of moving sliding windows of 50 nt along the whole genome was used to compare the normalized RNA-seq coverage (NRC) between the two strains. Using the standard whole gene differential expression analysis, significant upregulation of 5 genes in 4 operons was found in the sigH overexpressing strain. While with the sliding windiow analysis, 2 additional ÏH-dependent promoters were identified. Our results show that three ÏH-dependent transcritption units that encode competence proteins, including the comEABC , comGABCDEFG and coiA. Transcriptome profiles of L. monocytogenes 10403S::ÎBCHL Prha-sigH and ÎBCHL Prha were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.

2016-02-11 | E-GEOD-73008 | biostudies-arrayexpress