Diversity and signature of small RNA in different bodily fluids using next generation sequencing

BMC Genomics
Mohamed El-MogyYousef Haj-Ahmad

Abstract

Small RNAs are critical components in regulating various cellular pathways. These molecules may be tissue-associated or circulating in bodily fluids and have been shown to associate with different tumors. Next generation sequencing (NGS) on small RNAs is a powerful tool for profiling and discovery of microRNAs (miRNAs). In this study, we isolated total RNA from various bodily fluids: blood, leukocytes, serum, plasma, saliva, cell-free saliva, urine and cell-free urine. Next, we used Illumina's NGS platform and intensive bioinformatics analysis to investigate the distribution and signature of small RNAs in the various fluids. Successful NGS was accomplished despite the variations in RNA concentrations among the different fluids. Among the fluids studied, blood and plasma were found to be the most promising fluids for small RNA profiling as well as novel miRNA prediction. Saliva and urine yielded lower numbers of identifiable molecules and therefore were less reliable in small RNA profiling and less useful in predicting novel molecules. In addition, all fluids shared many molecules, including 139 miRNAs, the most abundant tRNAs, and the most abundant piwi-interacting RNAs (piRNAs). Fluids of similar origin (blood, urine or saliva...Continue Reading

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Citations

Jul 2, 2020·Nucleic Acids Research·Gal NechooshtanThomas R Gingeras
Jul 21, 2020·Head & Neck·Fiona T DeutschNham T Tran
Jun 12, 2020·World Journal of Gastroenterology : WJG·Karen ChiamDamian J Hussey
Oct 21, 2020·Toxicological Sciences : an Official Journal of the Society of Toxicology·Dongying LiBaitang Ning
Nov 6, 2020·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Jeremiah HoltYoon Ho Ko
Nov 20, 2020·International Journal of Molecular Sciences·Zuzana PösTomas Szemes
Sep 12, 2020·Molecular Therapy. Methods & Clinical Development·Laetitia S GasparLuís Pereira de Almeida
Apr 22, 2021·Proceedings of the National Academy of Sciences of the United States of America·Galina Yurevna ZheleznyakovaMaja Jagodic
Aug 8, 2021·Nanomaterials·Hiromi TakahashiYoshinobu Baba

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Methods Mentioned

BETA
chip
PCR
RNA-seq
PCA

Software Mentioned

VennDiagram
ggfortify
miRCarta
ComplexHeatmap
Genboree Workbench
R
FASTQC
Randfold
miRDeep2
R studio

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