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25 results for “Single-cell Proteomics”
pSCoPE: Prioritized Single-Cell Proteomics (data for generating publication figures)
<p>Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth of protein quantification, especially for proteins and modifications of biological interest. To simultaneously advance all these aims, we developed prioritized Single Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands of prioritized peptides across all single cells (thus increasing data completeness) while analyzing identifiable peptides at full duty-cycle, thus increasing proteome depth. These strategies increased the sensitivity, data completeness, and proteome coverage over 2-fold. The gains enabled quantifying protein variation in untreated and lipopolysaccharide-treated primary macrophages. Within each condition, proteins covaried within functional sets, including phagosome maturation and proton transport. This protein covariation within a treatment condition was similar across the treatment conditions and coupled to phenotypic variability in endocytic activity. pSCoPE also enabled quantifying proteolytic products, suggesting a gradient of cathepsin activities within a treatment condition. pSCoPE is freely available and widely applicable, especially for analyzing proteins of interest without sacrificing proteome coverage. Support for pSCoPE is available at: <a href="http://scp.slavovlab.net/pSCoPE">scp.slavovlab.net/pSCoPE</a></p> <p> </p> <p>The files contained in this .zip directory are necessary for replicating the analysis and figures associated with the pSCoPE manuscript.</p> <p> </p>
scProAtlas: an atlas of multiplexed single-cell spatial proteomics imaging in human tissues
<p>All analysis results for the spatial proteomics imaging techniques in the scProAtlas database are stored in compressed files named accordingly. Within each compressed file, the folders are organized in a fixed storage structure in the following order: Analysis module > Imaging Technique > Dataset > Tissue > ROI.</p> <p>Each folder contains the corresponding metadata (including original sample information, cell type annotations, and neighborhood annotations) stored in a file named <code>cells.tsv</code>. Additionally, the module used to identify spatial pattern genes includes an <code>anndata</code> format file, named <code>adata_moran.h5ad</code>, which stores the integrated results of scRNA-seq and spatial proteomics.</p> <p>scProAtlas_analysis_code.tar.gz contains example codes for all analysis modules in scProAtlas. Here, we provide the example using <strong>SCP_CODEX1 - Large intestine. </strong>The codes include all the scripts used for the entire workflow, from image segmentation to scRNA-spatial proteomics integration, and spatial analysis.</p> <p>We have also uploaded the raw protein channel matrices with AnnData format in <strong>version 3 and 4.</strong></p>
Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19
<p>The biological determinants underlying the range of COVID-19 clinical manifestations are not fully understood. Here, over 1400 plasma proteins and 2600 single-cell immune features comprising cell phenotype, endogenous signaling activity, and signaling responses to inflammatory ligands are cross-sectionally assessed in peripheral blood from 97 patients with mild, moderate, and severe COVID-19 and 40 uninfected patients. Using an integrated computational approach to analyze the combined plasma and single-cell proteomic data, we identify and independently validate a multivariate model classifying COVID-19 severity (multi-class AUC<sub>training</sub> = 0.799, p-value = 4.2e-6; multi-class AUC<sub>validation</sub> = 0.773, p-value = 7.7e-6). Examination of informative model features reveals novel biological signatures of COVID-19 severity, including the dysregulation of JAK/STAT, MAPK/mTOR, and NF-κB immune signaling networks in addition to recapitulating known hallmarks of COVID-19. These results provide a set of early determinants of COVID-19 severity that may point to therapeutic targets for prevention and/or treatment of COVID-19 progression.</p>
Resolving single-cell expression profiles by pseudo-temporal integration of transcriptomic and proteomic datasets.
<p>Raw and processed single cell proteomics (scp-MS) and scRNA-Seq data of HEK293-PIP-FUCCI cells which were challanged with hypoxia. The repository contains data for recreating the pseudo-temporal alignment analysis of transcription-translation profiles.</p>
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>
Integrated plasma proteomic and single-cell immune signaling network signatures demarcate mild, moderate, and severe COVID-19
Open the record for dataset details and reuse information.
Single-cell spatial transcriptomics and proteomics of APOE Christchurch in 5xFAD and PS19 mice
Open the record for dataset details and reuse information.
Single-cell TCA cycle proteomics of human embryos during early organogenesis
Open the record for dataset details and reuse information.
Immune Signature of Chronic Hand Eczema Unveiled by Spatial Transcriptomics and Single-Cell Proteomics
ClinicalTrials.gov study NCT06884163. IPD Sharing: NO. Countries: 1. Publications: 6.
Enhancing single-cell proteomics through tailored Data-Independent Acquisition and micropillar array-based chromatography
<p>This repository contains all the tables exported from Spectronaut.</p>
Data accompanying "Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using the scp package"
<p>Data and scripts accompanying the paper <em>Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using scp</em>.</p> <ul> <li>d.zip contains raw MS data from samples run on timsTOF SCP.</li> <li>raw.zip contains raw MS data from samples run on orbitrap mass spectrometers (Orbitrap Fusion Lumos Tribrid and Exploris 240).</li> <li>mzML.zip contains raw MS data in mzML format from all samples.</li> <li>sage.zip contains output results from the sage software (results.sage.tsv and quant.tsv) as well as configuration files (results.json) for both orbitrap (cbio) and timsTOF (giga) data.</li> <li>sample_annotation.zip contains csv files with samples annotation for each acquisition batch and used to build the colData.</li> <li>example_subset.zip contains csv files for short example datasets displayed in the paper.</li> <li>scp.rds file contains the initial QFeatures object of the full dataset with 56 PSM sets corresponding to the 56 MS runs.</li> <li>build_QF_dataset.Rmd file is the script used to build the scp.rds file described above from sage outputs and sample annotation.</li> </ul> <p>These file descriptions are also available in the README.txt file.</p>
CSF Single-cell Sequencing and Proteomics of Chronic Postsurgical Pain in Patients With Lower Limb Fractures
ClinicalTrials.gov study NCT06126289. IPD Sharing: Not stated. Countries: 0. Publications: 10.
Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains
GEO Series GSE202210. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
The dynamics of cellular response to therapeutic perturbation using multiplexed quantification of the proteome and transcriptome at single-cell resolution
GEO Series GSE100501. Homo sapiens. 31 samples. Type: Expression profiling by high throughput sequencing; Other.
A single-cell proteomic and transcriptomic assay identifies genes related to polyfunctionality of CAR-T cells targeting GPC1 in pancreatic cancer
GEO Series GSE220536. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Proteomic and single-cell transcriptomic dissection of human plasmacytoid dendritic cell response to influenza virus
GEO Series GSE189120. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Innate and adaptive immune responses to SARS-CoV-2 in Syrian hamsters disclosed by single-cell sequencing and high-throughput proteomics
GEO Series GSE162208. Mesocricetus auratus. 59 samples. Type: Expression profiling by high throughput sequencing.
Resolving single-cell gene expression by pseudo-temporal integration of transcriptomic and proteomic datasets.
GEO Series GSE273172. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNAseq and longitudinal proteomic analysis of a novel semi-spontaneous urothelial cancer model reveals tumor cell heterogeneity and pretumoral urine protein alterations
GEO Series GSE174182. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
Integrative Analysis of Exosome-Mediated Single-Cell Transcriptomics and Proteomics in Gastric Cardia Cancer
ClinicalTrials.gov study NCT06702891. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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.