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1,448 results for “proteomic”
Cancer-Associated Fibroblast Classification in Single-Cell and Spatial Proteomics Data
<p>ometiff: Imaging Data</p> <p>Cell Masks: Masks generated with cellprofiler from ilastik segmentation training</p> <p>cp-output_config: All relevant cellprofiler output and additional configuration files (for example clinical data) necessary to generate the single cell experiments.</p> <p>IMC Data Objects: Single cell experiment RDS files.</p> <p> </p> <p>scRNA-seq_dataobjects: .Rds files containing the clustered breast cancer, colon cancer, HNSCC, NSCLC and PDAC datasets as well as the integrated validation dataset.</p>
KidDO project update - quantitative proteomic and metabolomic analysis of five mouse models with chronic kidney disease
<p>Chronic kidney disease (CKD) is one of the most deadly diseases faced by patients and is a major global health and socioeconomic burden.CKD increases cardiovascular morbidity and premature mortality and decreases quality of life. Hypertension (HTN) and type 2 diabetes mellitus (T2DM), which are reaching epidemic levels, are major risk factors for CKD. CKD diagnosis and progression is based on estimated GFR (eGFR) and urinary albumin excretion. However, eGFR only has a predictive value in advanced disease and there is risk of progressive CKD in non-albuminuric individuals. Thus, there is an urgent need for new approaches for early detection of the most “at risk” individuals and identification of CKD signatures to aid in designing novel drugs and preventive measures that could ameliorate progression of CKD.</p> <p>Our overarching goal is to identify metabolites that predict kidney cell phenotypes during CKD and how crosstalk of these metabolites with the proteome drive CKD progression. We will integrate metabolomics and proteomic information from animal models of CKD with human CKD patient biopsies to identify common signatures in the tubulointerstitium that correlate with human pathophysiology.</p> <p>Here we provide quantitative proteomic and metabolomic datasets, as well as plasma and urine electrolyte measurements on five CKD mouse models.</p>
Processed results supporting MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics
<p>Search results supporting the manuscript "MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics". Processed PSM, ion, peptide, and protein tables for each search are provided, sorted by figure within the zip file. FragPipe workflows with parameters are also provided for all searches. </p>
Proteomic spectra of epipelagic copepods
<p><span>We analyzed robustness of species identification based on proteomic composition to data processing and intraspecific variability, specificity and sensitivity of species-markers as well as discriminatory power of proteomic fingerprinting and its sensitivity to phylogenetic distance. Our analysis is based on MALDI-TOF MS data from 32 marine copepod species coming from 13 regions (North and Central Atlantic and adjacent seas). </span>A random forest (RF) model correctly classified all specimens to species level with only small sensitivity to data processing, demonstrating the strong robustness of the method. Compounds with high specificity showed low sensitivity i.e., identification was based on complex pattern-differences rather than on presence of single markers.</p>
Data and analysis of proteomic responses to hexokinase-II depletion in GAL80 and gal80Δ Saccharomyces cerevisiae with an engineered sesquiterpene-pathway
<p>Dataset 1: <a href="https://zenodo.org/api/files/ece3309f-0ca2-4773-b2e3-b1c5c839faa4/GAL80_HXK2_Vs._dhxk2p_20200324_T2_004.xlsx">GAL80_HXK2_Vs._dhxk2p_20200324_T2_004.xlsx</a></p> <p>The comparison between strain ILHA o128R+pJT9RFR (dHxk2p) and ILHA o401R+ pJT9RFR (HXK2) under the conditions with the addition of 1-Naphthaleneacetic acid and in the exponential growth phase and the ethanol growth phase. </p> <p> </p> <p>Dataset 2: <a href="https://zenodo.org/api/files/ece3309f-0ca2-4773-b2e3-b1c5c839faa4/gal80%CE%94_HXK2_Vs._dhxk2p_20200219_T1_004.xlsx">gal80Δ_HXK2_Vs._dhxk2p_20200219_T1_004.xlsx</a></p> <p>The comparison between strain ILHA NLD128-1 (dHxk2p) and ILHA NLD401 (HXK2) under the conditions with the addition of 1-Naphthaleneacetic acid and in the exponential growth phase (EXP) and the ethanol growth phase (ETH). </p> <p> </p>
Proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility
<p>Full results datasets for Proteome association studies of breast, prostate, ovarian, and endometrial cancers implicate plasma protein regulation in cancer susceptibility:</p> <p>ALL*all_pheno.csv are TOPMed-MESA combined-ancestry models, discovery and replication cohorts</p> <p>ARIC_EA_all_pheno.csv is ARIC European-American ancestry models, discovery cohort</p> <p>ARIC*meta_all.txt is ARIC European-American ancestry models, discovery and replication cohorts, with meta-analysis of disc+rep</p>
The Role of Proteomics Analysis in Carcinogenesis in a Rat Mammary Cancer Model Induced by DMBA (7,12-dimethylbenz(α)anthracene)
<p>The dataset consists of raw data on protein concentration from a Nanodrop Spectrophotometer and raw data on protein molecular weight from SDS-PAGE</p>
Data sets for "Updated MS²PIP web server supports cutting-edge proteomics applications"
<p>Data sets and code used to train and evaluate new MS²PIP models. </p>
Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumor deposits in colorectal cancer
<p>Spatial transcriptomic data (counts_DSP_afterQC_normalisation.csv) derived using the Nanostring GeoMx digital spatial profiler platform to analyse tumor deposits and lymph node metastases from 10 patients with colorectal cancer. 264 AOIs of cancer transcriptome atlas data. Normalised using Q3 normalisation, for further information on methods see associated publication. </p>
The proteomics raw data from project MIPHA
<p>The proteomics data and search result from the hisD overexpression strains and control strains treated with or without levofloxacin. </p>
Proteomics analysis for: The platelet transcriptome and proteome in Alzheimer's disease and aging: an exploratory cross-sectional study
<p>Alzheimer’s disease (AD) and aging are associated with platelet hyperactivity. However, the mechanisms underlying abnormal platelet function in AD and aging are yet poorly understood. To explore the molecular profile of AD and aged platelets, we investigated platelet activation (i.e., CD62P expression), proteome and transcriptome in AD patients, non-demented elderly, and young individuals as controls. AD, aged and young individuals showed similar levels of platelet activation based on CD62P expression. However, AD and aged individuals had a proteomic signature suggestive of increased platelet activation compared with young controls. Transcriptomic profiling suggested the dysregulation proteolytic machinery involved in the regulation of platelet function, particularly in the ubiquitin-proteasome system in AD and autophagy in aging. The functional implication of these transcriptomic alterations remains unclear and requires further investigations. </p>
Code. Midlife proteome-wide analysis identifies plasma biomarkers for 25-year dementia risk linked to diverse pathophysiology
<p>The code used for the analyses for the paper entitled "Midlife proteome-wide analysis identifies plasma biomarkers for 25-year dementia risk linked to diverse pathophysiology". </p>
Immunoassay and proteomics dataset: Identification and validation of urine CXCL-9 as a biomarker for diagnosis of acute interstitial nephritis
<p>Background: Acute tubulointerstitial nephritis (AIN) is one of the few causes of acute kidney injury with diagnosis-specific treatment options. However, due to the need to obtain a kidney biopsy for histological confirmation, AIN diagnosis can be delayed, missed, or incorrectly assumed. Here we identify and validate urine CXCL-9, an interferon-γ-induced chemokine involved in lymphocyte chemotaxis, as a diagnostic biomarker for AIN.</p> <p>Methods: In a prospectively-enrolled cohort with pathologist-adjudicated histological diagnoses (<em>discovery cohort</em>), we tested the association of 180 immune proteins measured by an aptamer-based assay with AIN and validated the top protein, CXCL-9, using sandwich immunoassay. We externally validated these findings in 2 cohorts with biopsy-confirmed diagnoses (<em>validation cohorts</em>) and examined mRNA expression differences in kidney tissue from patients with AIN and controls.</p> <p>Results: In aptamer-based assay, urine CXCL-9 was 7.6-fold higher in AIN than controls (<em>P</em>=1.23·10<sup>-5</sup>). Urine CXCL-9 measured by sandwich immunoassay was associated with AIN in the discovery cohort (n=204; 15% AIN) independently of currently available clinical tests for AIN (adjusted odds ratio for highest vs lowest quartile: 6.0; 95% CI: 1.8-20). Similar findings were noted in external validation cohorts, where CXCL-9 had an AUC of 0.94 (0.86-1.00) for AIN diagnosis. <em>CXCL9</em> mRNA expression was 3.9-fold higher in kidney tissue from patients with AIN (n=19) as compared with controls (n=52; P=5.8·10<sup>-6</sup>).</p> <p>Conclusion: We identified CXCL-9 as a biomarker for AIN diagnosis using aptamer-based urine proteomics, confirmed this association using sandwich immunoassays in discovery and validation cohorts, and observed higher expression of this protein in kidney biopsies with AIN. </p>
MSFragger open searches of proteome shotgun and phosphoproteomic runs PXD013868 (Mergner et al., 2020)
<p>MSFragger open searches of phosphoproteomics and shotgun proteome runs of large-scale tissue atlas in Arabidopis (Mergner et al., 2020). Part of the Plant PTM Viewer 2.0 update paper.</p>
Analysis of the proteomic profile in serum of irradiated nonhuman primates treated with Ex-Rad, a radiation medical countermeasure
<p>There are currently four radiation medical countermeasures that have been approved by the United States Food and Drug Administration to mitigate hematopoietic acute radiation syndrome, all of which are repurposed radiomitigators. The evaluation of additional candidate drugs that may also be helpful for use during a radiological/nuclear emergency is ongoing. A chlorobenzyl sulfone derivative (organosulfur compound) known as Ex-Rad, or ON01210, is one such candidate medical countermeasure, being a novel, small-molecule kinase inhibitor that has demonstrated efficacy in the murine model. In this study, nonhuman primates exposed to ionizing radiation were subsequently administered Ex-Rad as two treatment schedules (Ex-Rad I administered 24 and 36 h post-irradiation, and Ex-Rad II administered 48 and 60 h post-irradiation) and the proteomic profiles of serum using a global molecular profiling approach were assessed. We observed that administration of Ex-Rad post-irradiation is capable of mitigating radiation-induced perturbations in protein abundance, particularly in restoring protein homeostasis and immune response and mitigating hematopoietic damage, at least in part after acute exposure. Taken together, restoration of functionally significant pathway perturbations may serve to protect damage to vital organs and provide long-term survival benefits to the afflicted population.</p>
Data from: Plasma proteomic signatures of enteric permeability among hospitalized and community children under two years of age in Kenya and Pakistan
<p class="MsoNormal">We aimed to establish if enteric permeability was associated with similar biological processes in children recovering from hospitalization and relatively healthy children in the community. Extreme gradient-boosted models predicting the lactulose rhamnose ratio, a biomarker of enteric permeability, using 7,500 plasma proteins and 34 fecal biomarkers of enteric infection among 89 hospitalized and 60 community children aged 2-23 months were built. The R<sup>2</sup> were calculated in test sets. The models performed better among community (R<sup>2</sup>: 0·27 [min-max: 0·19, 0·53]) than hospitalized children (R<sup>2</sup>: 0·07 [min-max: 0·03, 0·11]). In the community, LRR was associated with biomarkers of humoral antimicrobial and cellular lipopolysaccharide responses, and inversely associated with anti-inflammatory and innate immunological responses. Among hospitalized children, the selected biomarkers had few shared functions.<strong> </strong>This suggests enteric permeability among community children was associated with a host response to pathogens, but this association was not observed among hospitalized children.</p>
Data from: Potential of MALDI−TOF MS-based proteomic fingerprinting for species identification of Cnidaria across classes, species, regions and developmental stages
<p><span>Morphological identification of cnidarian species can be difficult throughout all life stages due to the lack of distinct morphological characters. Moreover, in some cnidarian taxa genetic markers are not fully informative, and in these cases combinations of different markers or additional morphological verifications may be required. Proteomic fingerprinting based on MALDI-TOF mass spectra was previously shown to provide reliable species identification in different metazoans including some cnidarian taxa. For the first time, we tested the method across four cnidarian classes (Staurozoa, Scyphozoa, Anthozoa, Hydrozoa) and included different scyphozoan life-history stages (polyp, ephyra, medusa) into our dataset. Our results revealed reliable species identification based on MALDI-TOF mass spectra across all taxa with species-specific clusters for all 23 analyzed species. In addition, proteomic fingerprinting was successful for distinguishing developmental stages, still by retaining a species specific signal. Furthermore, we identified the impact of different salinities in different regions (North Sea and Baltic Sea) on proteomic fingerprints to be negligible. In conclusion, the effects of environmental factors and developmental stages on proteomic fingerprints seem to be low in cnidarians. This would allow using reference libraries built up entirely of adult or cultured cnidarian specimens for the identification of their juvenile stages or specimens from different geographic regions in future biodiversity assessment studies.</span></p>
Genomic atlas of the human proteome from brain, CSF and plasma: Improvement with TOPMed imputed genomics
<p>Abstract</p> <p>Comprehensive expression quantitative trait loci (eQTL) studies have been instrumental for understanding tissue-specific gene regulation and pinpointing functional genes for disease-associated GWAS loci in a tissue-specific manner. Compared to gene expressions, proteins more directly affect various biological processes, often dysregulated in disease, and are important drug targets. We previously performed and identified tissue-specific protein QTL (pQTL) in neurologically relevant tissues. We now enhance this work by analyzing more proteins (1,300 versus 1,079) and an almost twofold increase in high-quality imputed genetic variants (8.4 million versus 4.4 million) by using TOPMed reference panel. We identified 38 genomic regions associated with 43 proteins in brain, 150 regions associated with 247 proteins in CSF, and 95 regions associated with 145 proteins in plasma. Compared to our previous study, this study newly identified 12 pQTL in brain, 30 pQTL in CSF, and 22 pQTL in plasma. Our improved genomic atlas uncovers the genetic control of protein regulation across multiple tissues. These pQTL findings are assessable through the Online Neurodegenerative Trait Integrative Multi-Omics Explorer (ONTIME) for use by the scientific community.</p>
Genomic atlas of the human proteome from brain, CSF and plasma: Improvement with TOPMed imputed genomics
<p>Abstract</p> <p>Comprehensive expression quantitative trait loci (eQTL) studies have been instrumental for understanding tissue-specific gene regulation and pinpointing functional genes for disease-associated GWAS loci in a tissue-specific manner. Compared to gene expressions, proteins more directly affect various biological processes, often dysregulated in disease, and are important drug targets. We previously performed and identified tissue-specific protein QTL (pQTL) in neurologically relevant tissues. We now enhance this work by analyzing more proteins (1,300 versus 1,079) and an almost twofold increase in high-quality imputed genetic variants (8.4 million versus 4.4 million) by using TOPMed reference panel. We identified 38 genomic regions associated with 43 proteins in brain, 150 regions associated with 247 proteins in CSF, and 95 regions associated with 145 proteins in plasma. Compared to our previous study, this study newly identified 12 pQTL in brain, 30 pQTL in CSF, and 22 pQTL in plasma. Our improved genomic atlas uncovers the genetic control of protein regulation across multiple tissues. These pQTL findings are assessable through the Online Neurodegenerative Trait Integrative Multi-Omics Explorer (ONTIME) for use by the scientific community.</p>
Genomic atlas of the human proteome from brain, CSF and plasma: Improvement with TOPMed imputed genomics
<p>Abstract</p> <p>Comprehensive expression quantitative trait loci (eQTL) studies have been instrumental for understanding tissue-specific gene regulation and pinpointing functional genes for disease-associated GWAS loci in a tissue-specific manner. Compared to gene expressions, proteins more directly affect various biological processes, often dysregulated in disease, and are important drug targets. We previously performed and identified tissue-specific protein QTL (pQTL) in neurologically relevant tissues. We now enhance this work by analyzing more proteins (1,300 versus 1,079) and an almost twofold increase in high-quality imputed genetic variants (8.4 million versus 4.4 million) by using TOPMed reference panel. We identified 38 genomic regions associated with 43 proteins in brain, 150 regions associated with 247 proteins in CSF, and 95 regions associated with 145 proteins in plasma. Compared to our previous study, this study newly identified 12 pQTL in brain, 30 pQTL in CSF, and 22 pQTL in plasma. Our improved genomic atlas uncovers the genetic control of protein regulation across multiple tissues. These pQTL findings are assessable through the Online Neurodegenerative Trait Integrative Multi-Omics Explorer (ONTIME) for use by the scientific community.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.