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      Advances and Trends in Omics Technology Development

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          Abstract

          The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.

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          Most cited references285

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          NCBI GEO: archive for functional genomics data sets—update

          The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.
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            Circular RNAs are a large class of animal RNAs with regulatory potency.

            Circular RNAs (circRNAs) in animals are an enigmatic class of RNA with unknown function. To explore circRNAs systematically, we sequenced and computationally analysed human, mouse and nematode RNA. We detected thousands of well-expressed, stable circRNAs, often showing tissue/developmental-stage-specific expression. Sequence analysis indicated important regulatory functions for circRNAs. We found that a human circRNA, antisense to the cerebellar degeneration-related protein 1 transcript (CDR1as), is densely bound by microRNA (miRNA) effector complexes and harbours 63 conserved binding sites for the ancient miRNA miR-7. Further analyses indicated that CDR1as functions to bind miR-7 in neuronal tissues. Human CDR1as expression in zebrafish impaired midbrain development, similar to knocking down miR-7, suggesting that CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript. Together, our data provide evidence that circRNAs form a large class of post-transcriptional regulators. Numerous circRNAs form by head-to-tail splicing of exons, suggesting previously unrecognized regulatory potential of coding sequences.
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              RNA-Seq: a revolutionary tool for transcriptomics.

              RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.
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                Author and article information

                Contributors
                Journal
                Front Med (Lausanne)
                Front Med (Lausanne)
                Front. Med.
                Frontiers in Medicine
                Frontiers Media S.A.
                2296-858X
                01 July 2022
                2022
                : 9
                : 911861
                Affiliations
                Wuxi School of Medicine, Jiangnan University , Wuxi, China
                Author notes

                Edited by: Roberto Gramignoli, Karolinska Institutet (KI), Sweden

                Reviewed by: Hector Quezada, Hospital Infantil de México Federico Gómez, Mexico; Mina Abedi, Tehran University of Medical Sciences, Iran

                *Correspondence: Xiaofeng Dai xiaofeng.dai@ 123456jiangnan.edu.cn

                This article was submitted to Translational Medicine, a section of the journal Frontiers in Medicine

                Article
                10.3389/fmed.2022.911861
                9289742
                35860739
                7d736be9-9095-40ae-81c9-7b0be88752a7
                Copyright © 2022 Dai and Shen.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 03 April 2022
                : 09 May 2022
                Page count
                Figures: 2, Tables: 1, Equations: 0, References: 286, Pages: 25, Words: 19439
                Funding
                Funded by: National Natural Science Foundation of China, doi 10.13039/501100001809;
                Funded by: Fundamental Research Funds for the Central Universities, doi 10.13039/501100012226;
                Categories
                Medicine
                Review

                omics,next generation sequencing,third generation sequencing,mass spectrometry,redoxomics

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