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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Ribosome Profiling02:24

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Related Experiment Video

Updated: Jun 12, 2025

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies
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A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

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Epigenomic, transcriptomic and proteomic characterizations of reference samples.

Chirag Nepal1,2, Wanqiu Chen1,2, Zhong Chen1,2

  • 1Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA.

Biorxiv : the Preprint Server for Biology
|September 24, 2024
PubMed
Summary
This summary is machine-generated.

New reference standards with multi-omics data, including epigenomics and proteomics, were developed for next-generation sequencing technologies. These standards aid in validating omics assays and bioinformatics methods for research and clinical applications.

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Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Epigenetics

Background:

  • Next-generation sequencing (NGS) technologies require accurate reference standards for research and clinical applications.
  • Previous studies provided genomic data but lacked comprehensive epigenomic and proteomic characterization.
  • A need exists for well-characterized reference materials integrating multiple omics data types.

Purpose of the Study:

  • To develop comprehensive reference materials with integrated genomic, epigenomic, transcriptomic, and proteomic data.
  • To characterize the epigenomic landscape and its overlap with transcriptomes and proteomes.
  • To provide standards for validating omics assays and bioinformatics methods.

Main Methods:

  • Performed ATAC-seq, Methyl-seq, RNA-seq, and proteomic analyses on two cell lines.
  • Analyzed somatic mutations, single-nucleotide variations (SNVs), and structural variations (SVs).
  • Investigated the relationship between open chromatin, DNA methylation, CG density, and gene/protein expression.

Main Results:

  • Generated a comprehensive catalog of the epigenomic landscape, overlapping with transcriptomes and proteomes.
  • Identified over 7,700 peptide isoforms, with most genes having a single isoform.
  • Observed higher protein expression for transcripts overlapping CpG islands (CGIs) and demonstrated SNVs in mutated peptides.
  • Found open chromatin regions with low methylation in CG-rich areas, correlating with higher gene and protein expression.
  • Identified cell line-specific methylation and gene expression patterns in CG-poor regions.

Conclusions:

  • Developed well-defined reference materials with multi-omics characterization for two cell lines.
  • These materials serve as valuable standards for validating and benchmarking omics assays and bioinformatics methods.
  • The resource will benefit both research and clinical communities by improving data accuracy and reproducibility.