Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TIMSTOF analysis of single human NCI-H-358 cells

ABSTRACT: SCOPE2 analysis of single human cells treated with a KRAS G12C inhibitor and analyzed on a TIMSTOF Flex instrument

INSTRUMENT(S): timsTOF fleX

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Benjamin C Orsburn

PROVIDER: MSV000087780 | MassIVE | Thu Jul 08 13:33:00 BST 2021

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

H358 single cell proteomics by SCOPE2 on a TIMSTOF Flex

Project description:Single H358 cells analyzed using SCOPE2 on a TIMSTOF Flex mass spectrometer. Bruker .d folders, MGFs, Proteome Discoverer 2.5 and MaxQuant 1.6.17 results are uploaded.

| MSV000088144 | MassIVE

MRTX1133 Mechanism of Action Study with Single Cell Proteomics

Project description:Bruker .d files in support of a multiomics analysis of the KRASG12D inhibitor MRTX1133. Files are broken into multiple repositories because uploading 3,000 single cell proteomes plus the bulk proteomics and the metabolomics and the metabolism stuff is really painful. This is the multiplexed (SCOPE2 on a TIMSTOF Flex) .d files for approximately 2,000 single human cells. Metadata will be provided in Orsburn, 2023

2023-01-22 | MSV000091112 | MassIVE

GNPS - MRTX1133 Mechanism of Action Study with Single Cell Proteomics

2023-01-22 | MSV000091112 | GNPS

10x Genomics scRNA-seq from monocytes and macrophages

Project description:The fate and physiology of individual cells are controlled by protein interactions. Yet, our ability to quantitatively analyze proteins in single cells has remained limited. To overcome this barrier, we developed SCoPE2. It lowers cost and hands-on time by introducing automated and miniaturized sample preparation while substantially increasing quantitative accuracy. These advances enabled us to analyze the emergence of cellular heterogeneity as homogeneous monocytes differentiated into macrophage-like cells in the absence of polarizing cytokines. SCoPE2 quantified over 2,700 proteins in 1,018 single monocytes and macrophages in ten days of instrument time, and the quantified proteins allowed us to discern single cells by cell type. Furthermore, the data uncovered a continuous gradient of proteome states for the macrophage-like cells, suggesting that macrophage heterogeneity may emerge even in the absence of polarizing cytokines. Parallel measurements of transcripts by 10x Genomics scRNA-seq suggest that SCoPE2 samples 20-fold more copies per gene, thus supporting quantification with improved count statistics. Joint analysis of the data indicated that most genes had similar responses at the protein and RNA levels, though the responses of hundreds of genes differed. Our methodology lays the foundation for automated and quantitative single-cell analysis of proteins by mass-spectrometry.

2019-12-20 | GSE142392 | GEO

Piper plants timsTOF fleX - MZmine 3 benchmark

Project description:Ethanolic extracts of piper plants (leafs, fruits) were dissolved in H2O/ACN (75/25) and analysed on a timsTOF fleX mass spectrometer.

| MSV000090327 | MassIVE

GNPS - Piper plants timsTOF fleX - MZmine 3 benchmark

Project description:Ethanolic extracts of piper plants (leafs, fruits) were dissolved in H2O/ACN (75/25) and analysed on a timsTOF fleX mass spectrometer.

| MSV000090327 | GNPS

Lessons learned in label free single cell proteomics on a TIMSTOF SCP system

Project description:This repository is an amalgamation of different single cells analyzed using label free approaches (both DDA/PASEF and DIAPASEF) on a TIMSTOF SCP system. Cells analyzed including multiple immoratalized cancer cell lines and primary human hepatocytes isolated from a single donor

2024-08-17 | MSV000095633 | MassIVE

Dynamic Single Cell Proteomics Reveals the Functional Shifts of Dermal Sheath Cells during Wound Healing

Project description:Single-cell proteomics data of dermal sheath cells (DSCs) during wound healing, generated using SCoPE2-MS, highlighting dynamic protein expression and functional changes across different healing stages.

2024-10-28 | PXD057239 |

Single cell RNA-seq of pancreatic mouse tumors upon treatment

Project description:KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) is highly immunosuppressive and resistant to targeted therapies, immune checkpoint blockade and engineered T cells. In this study, we performed a systematic high throughput combinatorial drug screen and identified a synergistic interaction between the MEK inhibitor trametinib and the multi- kinase inhibitor nintedanib. Using single cell RNA sequencing and immunophenotyping, we show that the combination therapy reprograms the immunosuppressive microenvironment and primes cytotoxic and memory T cells to infiltrate the tumors, thereby sensitizing mesenchymal PDAC to PD-L1 inhibition.

2021-11-13 | E-MTAB-9954 | biostudies-arrayexpress

SCoPE2 - Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity - massive.quant

Project description:The fate and physiology of individual cells are controlled by proteins. Yet, our ability to quantitatively analyze proteins in single cells has remained limited. To overcome this barrier, we developed SCoPE2. It substantially increases quantitative accuracy and throughput while lowering cost and hands-on time by introducing automated and miniaturized sample preparation. These advances enabled us to analyze the emergence of cellular heterogeneity as homogeneous monocytes differentiated into macrophage-like cells in the absence of polarizing cytokines. SCoPE2 quantified over 3,042 proteins in 1,490 single monocytes and macrophages in ten days of instrument time, and the quantified proteins allowed us to discern single cells by cell type. Furthermore, the data uncovered a continuous gradient of proteome states for the macrophage-like cells, suggesting that macrophage heterogeneity may emerge even in the absence of polarizing cytokines. Parallel measurements of transcripts by 10x Genomics scRNA-seq suggest that our measurements sampled 20-fold more protein copies than RNA copies per gene, and thus SCoPE2 supports quantification with improved count statistics. Joint analysis of the data illustrates how variability across single cells can reveal transcriptional and post-transcriptional gene regulation. Our methodology lays the foundation for automated and quantitative single-cell analysis of proteins by mass-spectrometry.

2020-12-08 | MSV000086570 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data