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Proteome of extracellular vesicles derived from MCF-10A and MDA-MB-231 cells

ABSTRACT: Proteins in the EVs of MCF-10A and MDA-MB-231 cells were determined by mass spectrometry at Beijing Proteome Research Center using a LC-MS/MS platform comprising a nanoflow high-performance liquid chromatograph (HPLC) instrument (EASY-nLC 1000 nanoflow LC, Thermo Scientific, USA) coupled with a LTQ Orbitrap Velos mass spectrometer (Thermo Scientific, USA).

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Mcf-10a Cell, Mda-mb-231 Cell

SUBMITTER: haifeng zhou

LAB HEAD: Wei Yan

PROVIDER: PXD069253 | Pride | 2025-10-10

REPOSITORIES: Pride

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Project description:Probing epigenetic features on long molecules of DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA using GpC methyltransferase to exogenously label open chromatin, coupled with nanopore sequencing technology. We performed nanopore sequencing of Nucleosome Occupancy and Methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231), and demonstrate the ability to directly measure methylation and chromatin accessibility in genomic features such as structural variations and repetitive elements. The long single-molecule resolution allows footprinting of protein and nucleosome binding and determining the combinatorial promoter epigenetic state on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, enabling allele-specific epigenetic analysis across the genome. We use existing SNV data on GM12878 to present the first fully phased human Probing epigenetic features on long molecules of DNA has tremendous potential to advance our understanding of the phased epigenome. We evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA using GpC methyltransferase to exogenously label open chromatin, coupled with nanopore sequencing technology. We performed nanopore sequencing of Nucleosome Occupancy and Methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231), and demonstrate the ability to directly measure methylation and chromatin accessibility in genomic features such as structural variations and repetitive elements. The long single-molecule resolution allows footprinting of protein and nucleosome binding and determining the combinatorial promoter epigenetic state on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, enabling allele-specific epigenetic analysis across the genome. We use existing SNV data on GM12878 to present the first fully phased human epigenome, consisting of chromosome-level allele-specific profiles of CpG methylation and chromatin accessibility.mosome-level allele-specific profiles of CpG methylation and chromatin accessibility.

			Action	DRS
	10A_EV_1.raw	Raw
	10A_EV_2.raw	Raw
	10A_EV_3.raw	Raw
	231_EV_1.raw	Raw
	231_EV_2.raw	Raw

Dataset Information

Proteome of extracellular vesicles derived from MCF-10A and MDA-MB-231 cells

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