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One-pot method for preparing DNA, RNA, and protein for multiomics analysis

ABSTRACT: One-pot method for preparing DNA, RNA, and protein for multiomics analysis

PROVIDER: PRJNA1008152 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR25734029_1.fastq.gz	Fastqsanger.gz
	SRR25734029_2.fastq.gz	Fastqsanger.gz
	SRR25734030_1.fastq.gz	Fastqsanger.gz
	SRR25734030_2.fastq.gz	Fastqsanger.gz
	SRR25734031_1.fastq.gz	Fastqsanger.gz

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Project description:Typical multiomics studies employ separate methods for DNA, RNA, and protein sample preparation, which is labor intensive, costly, and prone to sampling bias. We describe a method for preparing high-quality, sequencing-ready DNA and RNA, and either intact proteins or mass-spectrometry-ready peptides for whole proteome analysis from a single sample. This method utilizes a reversible protein tagging scheme to covalently link all proteins in a lysate to a bead-based matrix and nucleic acid precipitation and selective solubilization to yield separate pools of protein and nucleic acids. We demonstrate the utility of this method to compare the genomes, transcriptomes, and proteomes of four triple-negative breast cancer cell lines with different degrees of malignancy. These data show the involvement of both RNA and associated proteins, and protein-only dependent pathways that distinguish these cell lines. We also demonstrate the utility of this multiomics workflow for tissue analysis using mouse brain, liver, and lung tissue.

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Project description:Investigate if one-pot analysis works on several energetic-based proteomics method on cyclosporine A.

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A chemoenzymatic method for simultaneous profiling N- and O-glycans on glycoproteins using one-pot format

Project description:Glycosylation, including N-glycosylation and O-glycosylation is generally characterized and controlled as a critical quality attribute for therapeutic glycoproteins because glycans can impact protein-based drug product efficacy, half-life, stability, and safety. Analytical procedures to characterize N-glycans are relatively well-established, but the characterization of O-glycans is challenging due to the complex workflows and lack of enzymatic tools. Here we present a simplified chemoenzymatic method to simultaneously profile N- and O-glycans from the same sample using a one-pot format by mass spectrometry (MS). N-glycans were first released by PNGase F, followed by O-glycopeptide generation by Proteinase K, selective N-glycan reduction, and O-glycan release by β-elimination during permethylation of both N- and O- glycans. Glycan structural assignments, and determination of N- to O-glycan ratio was obtained from the one-pot mass spectra. The streamlined, one-pot method is an accurate and reproducible approach that will facilitate advanced characterizations for quality assessments of therapeutic glycoproteins.

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‘One-pot’ sample processing method for proteome-wide analysis of microbial cells and spores

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