Optimizing a massive parallel sequencing workflow for quantitative miRNA expression analysis.

PloS One
Francesca CorderoRaffaele A Calogero

Abstract

Massive Parallel Sequencing methods (MPS) can extend and improve the knowledge obtained by conventional microarray technology, both for mRNAs and short non-coding RNAs, e.g. miRNAs. The processing methods used to extract and interpret the information are an important aspect of dealing with the vast amounts of data generated from short read sequencing. Although the number of computational tools for MPS data analysis is constantly growing, their strengths and weaknesses as part of a complex analytical pipe-line have not yet been well investigated. A benchmark MPS miRNA dataset, resembling a situation in which miRNAs are spiked in biological replication experiments was assembled by merging a publicly available MPS spike-in miRNAs data set with MPS data derived from healthy donor peripheral blood mononuclear cells. Using this data set we observed that short reads counts estimation is strongly under estimated in case of duplicates miRNAs, if whole genome is used as reference. Furthermore, the sensitivity of miRNAs detection is strongly dependent by the primary tool used in the analysis. Within the six aligners tested, specifically devoted to miRNA detection, SHRiMP and MicroRazerS show the highest sensitivity. Differential expressio...Continue Reading

References

Oct 1, 1978·Seminars in Nuclear Medicine·C E Metz
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Feb 20, 2003·RNA·Victor AmbrosThomas Tuschl
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Kim R RasmussenEugene W Myers
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Nov 10, 2007·Nucleic Acids Research·Sam Griffiths-JonesAnton J Enright
Apr 9, 2008·Nature Biotechnology·Marc R FriedländerNikolaus Rajewsky
May 10, 2008·Bioinformatics·Kay PrüferJanet Kelso
Aug 21, 2008·Bioinformatics·Simon MoxonVincent Moulton
Dec 2, 2008·BMC Genomics·Cristina Della BeffaRaffaele A Calogero
Jan 16, 2009·BMC Genomics·Damian SmedleyArek Kasprzyk
May 13, 2009·Nucleic Acids Research·Michael HackenbergAna M Aransay
May 23, 2009·PLoS Computational Biology·Stephen M RumbleMichael Brudno
Jul 14, 2009·Genome Research·David WeeseKnut Reinert
Nov 3, 2009·Bioinformatics·Anne-Katrin EmdeSilke R Sperling
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
May 13, 2010·BMC Bioinformatics·Lihua J ZhuMichael R Green
Aug 12, 2010·BMC Bioinformatics·Thomas J Hardcastle, Krystyna A Kelly
Aug 31, 2010·Bioinformatics·Roy RonenNoam Shomron
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Bogdan PaşaniucEran Halperin
Jul 14, 2011·Genome Research·Shahar AlonEli Eisenberg
Jul 21, 2011·BMC Bioinformatics·Wei ZhengHongyu Zhao
Sep 6, 2011·Nucleic Acids Research·Anitha D JayaprakashRavi Sachidanandam

❮ Previous
Next ❯

Citations

Apr 27, 2013·BMC Bioinformatics·Thomas J Hardcastle, Krystyna A Kelly
Dec 4, 2015·Nature Communications·Aliza P WingoKerry J Ressler
Jun 20, 2015·Frontiers in Bioengineering and Biotechnology·Dario VenezianoAlfredo Ferro
Oct 7, 2014·PloS One·Veronica ColangeloRaffaella Meneveri
Sep 1, 2017·Allergy·V D'ArgenioR Berni Canani
Jun 9, 2020·Clinical and Translational Medicine·Kira GroenJeannette Lechner-Scott
May 2, 2018·Frontiers in Endocrinology·Azliana Mohamad YusofNurul-Syakima Ab Mutalib
Jun 18, 2020·Frontiers in Immunology·Cristina LecchiFabrizio Ceciliani
Apr 4, 2021·International Journal of Molecular Sciences·Daisy SprovieroCristina Cereda
Jul 21, 2021·Scientific Reports·Edoardo BardiCristina Lecchi

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE14511

Methods Mentioned

BETA
RNA-seq
PCR
miRNA-seq

Software Mentioned

miRExpress
ENSEMBL
RazerS
MPS
SHRIMP
DESeq
SAM
baySeq package
R script
MicroRaserS

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.