Dataset Information

Comparative proteomic profiling of target DNA probe-associated proteins in MCF-7 cells

ABSTRACT: This dataset contains label-free quantitative LC-MS/MS data from a comparative DNA affinity pull-down experiment. Two different 5′-biotinylated DNA probes were incubated with nuclear protein extracts from MCF-7 cells. Probe-associated protein complexes were enriched with streptavidin magnetic beads, eluted, digested and analyzed by nanoflow LC-MS/MS. Protein abundance in the target-probe group was compared with that in the reference-probe group to identify proteins showing preferential association with the selected DNA sequence. The submitted files include raw mass spectrometry data and processed protein identification and quantification results.

ORGANISM(S): Homo Sapiens

SUBMITTER: Shuang Yang

PROVIDER: PXD081675 | iProX | Sun Jul 26 00:00:00 GMT+01:00 2026

REPOSITORIES: iProX

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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.

Dataset Information

Comparative proteomic profiling of target DNA probe-associated proteins in MCF-7 cells

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