RNA Sequencing

Lucchinetti, Eliana; Zaugg, Michael

doi:10.1097/aln.0000000000003524

Cited by 5 publications

(4 citation statements)

References 13 publications

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“…Next-generation sequencing (NGS) has had a transformative impact on transcriptomics, revolutionizing our ability to study the transcriptome-the complete set of RNA molecules in an organism or specific cell population. NGS technologies offer high-throughput and cost-effective methods for profiling and analyzing RNA molecules, allowing researchers to gain deep insights into gene expression, alternative splicing, non-coding RNA regulation, and various biological processes and diseases [40][41][42][43]. Here are some key roles of NGS in transcriptomics:…”

Section: Transcriptomicsmentioning

confidence: 99%

Next-Generation Sequencing Technology: Current Trends and Advancements

Satam,

Joshi,

Mangrolia

et al. 2023

Biology

282

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The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules in a high-throughput and cost-effective manner. This transformative technology has swiftly propelled genomics advancements across diverse domains. NGS allows for the rapid sequencing of millions of DNA fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, and epigenetic modifications. The versatility of NGS platforms has expanded the scope of genomics research, facilitating studies on rare genetic diseases, cancer genomics, microbiome analysis, infectious diseases, and population genetics. Moreover, NGS has enabled the development of targeted therapies, precision medicine approaches, and improved diagnostic methods. This review provides an insightful overview of the current trends and recent advancements in NGS technology, highlighting its potential impact on diverse areas of genomic research. Moreover, the review delves into the challenges encountered and future directions of NGS technology, including endeavors to enhance the accuracy and sensitivity of sequencing data, the development of novel algorithms for data analysis, and the pursuit of more efficient, scalable, and cost-effective solutions that lie ahead.

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Section: Transcriptomicsmentioning

confidence: 99%

Next-Generation Sequencing Technology: Current Trends and Advancements

Satam,

Joshi,

Mangrolia

et al. 2023

Biology

282

View full text Add to dashboard Cite

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“…Transcriptome refers to the sum of all RNAs transcribed in a specific tissue or cell at a certain time or state, mainly including mRNA and non-coding RNA [ 5 ]. RNA sequencing is based on Illumina sequencing platform to study all mRNA transcribed in a specific tissue or cell at a definite period [ 6 ]. It is the basis of gene function and structure research, and plays a major role in understanding the development of organisms and the occurrence of diseases.…”

Section: Introductionmentioning

confidence: 99%

Screening of key genes in the pathogenesis of muscle atrophy in CKD-PEW children based on RNA sequencing

Ying,

Yeping,

Hui

et al. 2023

BMC Med Genomics

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Background In children with CKD, Protein Energy Wasting (PEW) is common, which affects the outcome of children and is an important cause of poor prognosis. We are aiming to explore the pathogenesis of muscle wasting in CKD-PEW children. Methods Blood samples of 32 children diagnosed with chronic kidney disease (CKD) and protein energy wasting (PEW) in our hospital from January 2016 to June 2021 were collected. RNA sequencing and bioinformatics analysis were performed. Results Based on GO (Gene Ontology) functional enrichment analysis, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis and differential gene expression analysis, a total of 25 CKD-PEW related genes were obtained including CRP, IL6, TNF, IL1B, CXCL8, IL12B, IL12A, IL18, IL1A, IL4, IL10, TGFB2, TGFB1, TGFB3, ADIPOQ, NAMPT, RETN, RETNLB, LEP, CD163, ICAM1, VCAM1, SELE, NF-κB1, NF-κB2. The most significantly differentially expressed gene was NF-κB2 (adjusted P = 2.81 × 10–16), and its expression was up-regulated by 3.92 times (corresponding log2FoldChange value was 1.979). Followed by RETN (adjusted P = 1.63 × 10–7), and its expression was up-regulated by 8.306 times (corresponding log2FoldChange value was 2.882). SELE gene were secondly significant (adjusted P = 5.81 × 10–7), and its expression was down-regulated by 22.05 times (corresponding log2FoldChange value was -4.696). Conclusions A variety of inflammatory factors are involved in the pathogenesis of CKD-PEW in children, and chronic inflammation may lead to the development of muscle atrophy in CKD-PEW. It is suggested for the first time that NF-κB is a key gene in the pathogenesis of muscle wasting in CKD-PEW children, and its increased expression may play an important role in the pathogenesis of muscle wasting in children with CKD-PEW.

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“…Conventional miRNA detection methods include quantitative real-time polymerase chain reaction (qRT-PCR), Northern blotting, in situ hybridization, and RNA sequencing [6][7][8][9], and so on. For instance, Mikael et al [10] proposed a highly specific, sensitive, and costeffective system based on two-step RT-qPCR and SYBR Green detection chemistry, called 2 of 13 "two-tailed RT-qPCR", for quantitative miRNA expression.…”

Section: Introductionmentioning

confidence: 99%

Programmable, Universal DNAzyme Amplifier Supporting Pancreatic Cancer-Related miRNAs Detection

Nie

Jiang²,

Wang³

et al. 2022

Chemosensors

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The abnormal expression of miRNA is closely related to the occurrence of pancreatic cancer. Herein, a programmable DNAzyme amplifier for the universal detection of pancreatic cancer-related miRNAs was proposed based on its programmability through the rational design of sequences. The fluorescence signal recovery of the DNAzyme amplifier showed a good linear relationship with the concentration of miR-10b in the range of 10–60 nM, with a detection limit of 893 pM. At the same time, this method displayed a high selectivity for miR-10b, with a remarkable discrimination of a single nucleotide difference. Furthermore, this method was also successfully used to detect miR-21 in the range of 10–60 nM based on the programmability of the DNA amplifier, exhibiting the universal application feasibility of this design. Overall, the proposed programmable DNAzyme cycle amplifier strategy shows promising potential for the simple, rapid, and universal detection of pancreatic cancer-related miRNAs, which is significant for improving the accuracy of pancreatic cancer diagnosis.

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RNA Sequencing

Abstract: This editorial accompanies the article on p. 1060.

Cited by 5 publications

References 13 publications

Next-Generation Sequencing Technology: Current Trends and Advancements

Next-Generation Sequencing Technology: Current Trends and Advancements

Screening of key genes in the pathogenesis of muscle atrophy in CKD-PEW children based on RNA sequencing

Programmable, Universal DNAzyme Amplifier Supporting Pancreatic Cancer-Related miRNAs Detection

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