RNA-Seq Experiment and Data Analysis

Withanage, Miyuraj Harishchandra Hikkaduwa; Liang, Hanquan; Zeng, Erliang

doi:10.1007/978-1-0716-1920-9_22

Cited by 13 publications

(9 citation statements)

References 17 publications

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“…The ligation products were reverse transcribed by PCR amplification, and the 140-160 bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeq Xten by Gene Denovo Biotechnology Co. (Guangzhou, China). [14]. Reads obtained from the sequencing machines were filtered to get clean tags, and all the clean tags were aligned with small RNAs in GenBank database (Release 209.0) and Rfam database (Release 11.0) to identify and remove rRNA, scRNA, sonRNA, snRNA, and tRNA.…”

Section: Methodsmentioning

confidence: 99%

RNA-Sequence Reveals the Regulatory Mechanism of miR-149 on Osteoblast Skeleton under Mechanical Tension

Wang

Zhu

Fang

et al. 2022

Stem Cells International

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Objective. Based on RNA-sequencing (RNA-seq), the regulation of miRNAs differentially expressed in dental, periodontal, and alveolar bone tissue of orthodontic tree shrews on osteoblast skeleton under tension was investigated. Methods. Tree shrews were used to construct orthodontic models. We used RNA-seq to identify differentially expressed miRNAs in periodontal tissues of the treatment group and control group tree shrews. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for enrichment analysis. Human osteoblast MG63 was treated with 5000 U mechanical tension. Real-time quantitative polymerase chain reaction (RT-qPCR) detected the expression of miR-149 and ARFGAP with SH3 domain, Ankyrin repeat, and Ph domain 3 (ASAP3) mRNA. Western blot detected the protein levels of ASAP3, F-actin, osteogenic markers bone morphogenetic protein 2 (BMP2), and runt-related transcription factor 2 (RUNX2). Rhodamine phalloidin was used to observe the fluorescence intensity of F-actin. Validation of the targeting relationship between miR-149 and ASAP3 by dual luciferase reporter gene assay. Results. By performing miRNA-seq analysis on the dental and periodontal tissue of tree shrews in the treatment group and control group, we identified 51 upregulated miRNAs and 13 downregulated miRNAs. The expression of miR-149 in the dental and periodontal tissue of tree shrew and MG63 cells treated with mechanical tension was decreased, and miR-149 targeted ASAP3. Knockdown of ASAP3 inhibited the fluorescence intensity of F-actin in MG63 cells treated with 5000 U tension for 36 h, and overexpression of ASAP3 promoted the expression of F-actin and osteogenic markers BMP2 and RUNX2. Conclusions. These findings revealed that miR-149 could modulate osteoblast differentiation under orthodontics mechanical tension through targeting ASAP3.

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Section: Methodsmentioning

confidence: 99%

RNA-Sequence Reveals the Regulatory Mechanism of miR-149 on Osteoblast Skeleton under Mechanical Tension

Wang

Zhu

Fang

et al. 2022

Stem Cells International

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“…In addition, we also detected the average quality distribution of sequencing data through the average quality distribution of Reads to observe the overall quality of Reads. The results showed that the quality of sequencing data was good, which met the requirements of further experimental analysis [22] .…”

Section: Discussionmentioning

confidence: 65%

Research on protein and peptides in scorpion based on transcriptomics- proteomics-peptidomics integrated association analysis strategy

Gao,

Li,

Zhao

et al. 2024

Preprint

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Background: To preliminarily elucidate the possible molecular basis of scorpion efficacy through the methods of transcriptomic-proteomic-peptidomics. Methods: The transcriptome data of scorpion were obtained by high-throughput sequencing and analyzed by bioinformatics to establish the protein prediction database of scorpion. Furthermore, the proteomics and peptidomics of scorpion were analyzed by LC-MS analysis, and the GO annotation and KEGG pathway function enrichment analysis were performed for the identified proteins to explore the material basis of the efficacy of scorpion. Results: A total of 17605 gene sequences were obtained by transcriptome sequencing, and 12368 proteins could be predicted. 278 transcription factors and 51 family information of transcription factors were obtained through database comparison. From GO and KEGG annotation results, it was found that scorpion had functions such as regulating cell cycle, amino acid metabolism and signal transduction, which may be closely related to the analgesic and anti-cancer functions of scorpion. In the process of proteome identification, 10,072 peptides were found, and 1917 protein components were deduced from these peptides. For the identification of peptides, 6758 peptides were matched in the transcriptome database and 33,834 peptides were identified by de novo sequencing. The results showed that the scorpion proteins were mainly enriched in protein translation, tricarboxylic acid cycle and glycolysis, and the KEGG pathway was mainly enriched in oxidative phosphorylation, amino acid metabolism and ribosome. Conclusions: A total of 33834 peptides and 1917 proteins were identified from scorpion by integrated transcriptomic-proteomics-peptidomics association analysis. GO annotation and KEGG pathway functional enrichment analysis showed that the macromolecular components of scorpion were mainly related to oxidative phosphorylation, amino acid metabolism and immune regulation.

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“…Biosensor [ 33 ] and microarray [ 34 ] methods are known for hybridizing microRNAs, enabling the simultaneous detection of a large number (hundreds or thousands) of microRNA targets. High-throughput sequencing (Sanger sequencing or next-generation sequencing) [ 35 ] is used to identify new microRNA sequences.…”

Section: Methods For Assessing the Pool And Mirna Expressionmentioning

confidence: 99%

The Role of microRNAs in Epigenetic Regulation of Signaling Pathways in Neurological Pathologies

Tregub,

Ibrahimli,

Averchuk

et al. 2023

IJMS

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In recent times, there has been a significant increase in researchers’ interest in the functions of microRNAs and the role of these molecules in the pathogenesis of many multifactorial diseases. This is related to the diagnostic and prognostic potential of microRNA expression levels as well as the prospects of using it in personalized targeted therapy. This review of the literature analyzes existing scientific data on the involvement of microRNAs in the molecular and cellular mechanisms underlying the development of pathologies such as Alzheimer’s disease, cerebral ischemia and reperfusion injury, and dysfunction of the blood–brain barrier.

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RNA-Seq Experiment and Data Analysis

Cited by 13 publications

References 17 publications

RNA-Sequence Reveals the Regulatory Mechanism of miR-149 on Osteoblast Skeleton under Mechanical Tension

RNA-Sequence Reveals the Regulatory Mechanism of miR-149 on Osteoblast Skeleton under Mechanical Tension

Research on protein and peptides in scorpion based on transcriptomics- proteomics-peptidomics integrated association analysis strategy

The Role of microRNAs in Epigenetic Regulation of Signaling Pathways in Neurological Pathologies

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