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The RNA workbench 2.0: next generation RNA data analysis

2019 Nucleic Acids Research  
RNA-Seq experiments and methods for e.g. target predictions. To address these needs, we present the RNA Workbench 2.0 , an updated online resource for RNA related analysis.  ...  With the RNA Workbench we created a comprehensive set of analysis tools and workflows that enables researchers to analyze their data without the need for sophisticated command-line skills.  ...  their tools into the RNA Workbench 2.0 and accepted patches and to whom we wish a wonderful day, every day.  ... 
doi:10.1093/nar/gkz353 pmid:31073612 pmcid:PMC6602469 fatcat:gcrie4lr6nhitclbb56hcglyje

Transcriptome Analysis of Feline Infectious Peritonitis Virus Infection [chapter]

Parvaneh Mehrbod, Mohammad Syamsul Reza Harun, Ahmad Naqib Shuid, Abdul Rahman Omar
2015 Msphere  
Here, we describe the sequencing of RNA extracted from Crandell Rees Feline Kidney (CRFK) cells infected with FIPV using the Illumina next-generation sequencing approach.  ...  Kal's Z test statistical analysis is used to analyze the differentially expressed genes from the infected CRFK cells.  ...  The funding source has no role in this study.  ... 
doi:10.1007/978-1-4939-2438-7_20 pmid:25720485 pmcid:PMC7121011 fatcat:cyq7salnpfclfa5u43c4dqlthy

Integrated Transcriptome and Pathway Analyses Revealed Multiple Activated Pathways in Breast Cancer

Radhakrishnan Vishnubalaji, Varun Sasidharan Nair, Khalid Ouararhni, Eyad Elkord, Nehad M. Alajez
2019 Frontiers in Oncology  
A selected number of genes from the RNA-Seq analysis were subsequently validated using qRT-PCR.  ...  Differentially expressed (2.0-fold change, adj. p < 0.05) transcripts were subjected to ingenuity pathway analysis, which revealed a myriad of affected signaling pathways and functional categories.  ...  ACKNOWLEDGMENTS We thank the genomic core facility at Qatar Biomedical Research Institute for their help with RNA sequencing.  ... 
doi:10.3389/fonc.2019.00910 pmid:31620367 pmcid:PMC6759650 fatcat:o2qpwmo2ebezjdjgk7yehc6pb4

Glycogene Expression Profiling of Hepatic Cells by RNA-Seq Analysis for Glyco-Biomarker Identification

Kiyohiko Angata, Hiromichi Sawaki, Shigeko Tsujikawa, Makoto Ocho, Akira Togayachi, Hisashi Narimatsu
2020 Frontiers in Oncology  
Both data sets indicated that altered expression of glycosyltransferases affect the glycosylation of particular glycoproteins, which is consistent with the mass analysis data.  ...  the expression level of biomarkers might not be altered, the expression of the glycogenes modifying biomarkers, generating glyco-biomarkers, might be different.  ...  Suzuki in the Glycoscience and Glycotechnology Research Group at AIST for helping with the bioinformatics analysis. We would like to thank Editage for English language editing.  ... 
doi:10.3389/fonc.2020.01224 pmid:32850363 pmcid:PMC7402167 fatcat:wesdms5frng4zmwmhc66eianv4

Detection of a pneumonia virus of mice (PVM) in an African hedgehog (Atelerix arbiventris) with suspected wobbly hedgehog syndrome (WHS)

Hiroo Madarame, Kikumi Ogihara, Moe Kimura, Makoto Nagai, Tsutomu Omatsu, Hideharu Ochiai, Tetsyuya Mizutani
2014 Veterinary Microbiology  
Jonathan Lynch for English proofreading of the original manuscript.  ...  This research work was partially supported by a Grant-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology of Japan (no. 23580414).  ...  homology by analysis of next generation sequencing).  ... 
doi:10.1016/j.vetmic.2014.07.012 pmid:25129384 fatcat:su6c6s6yc5dtjdzrtyvwkbyzue

Double-stranded RNA binding protein, Staufen, is required for the initiation of RNAi in coleopteran insects

June-Sun Yoon, Kanakachari Mogilicherla, Dhandapani Gurusamy, Xien Chen, Shankar C. R. R. Chereddy, Subba Reddy Palli
2018 Proceedings of the National Academy of Sciences of the United States of America  
2 Data S1 The list of the genes downregulated in RNA-seq data based on the differential expression of gene expression analysis between Lepd-SL1 and Lepd-SL1RR.  ...  Data S2 The list of the genes upregulated in RNA-seq data based on the differential expression of gene expression analysis between Lepd-SL1 and Lepd-SL1RR.  ... 
doi:10.1073/pnas.1809381115 pmid:30061410 pmcid:PMC6099913 fatcat:i6flfqsuhrc6phpynjw3yho66u

Genomic analysis ofSaccharomyces cerevisiaeisolates that grow optimally with glucose as the sole carbon source

Anthony D. Aragon, Norah Torrez-Martinez, Jeremy S. Edwards
2012 Electrophoresis  
After the evolution period three single colony isolates were selected for analysis. Next-generation Ion Torrent sequencing was used to evaluate genetic changes.  ...  Affymetrix DNA microarrays and RNseq analysis were used to determine differences in gene expression in the evolved strains compared to the parental strain.  ...  Acknowledgments Some experiments used the facilities or services provided by the Keck-UNM Genomics Resource, a facility supported by a grant from the WM Keck Foundation as well as the State of New Mexico  ... 
doi:10.1002/elps.201200172 pmid:23135695 pmcid:PMC3822012 fatcat:6uf3ck2okvfk7kqibqpdxlqrwe

Equine Encephalosis Virus in India, 2008

Pragya D. Yadav, César G. Albariño, Dimpal A. Nyayanit, Lisa Guerrero, M. Harley Jenks, Prasad Sarkale, Stuart T. Nichol, Devendra T. Mourya
2018 Emerging Infectious Diseases  
A virus isolated from a sick horse from India in 2008 was confirmed by next-generation sequencing analysis to be equine encephalosis virus (EEV).  ...  Acknowledgments We thank the authority of the horse stud farm in Pune for providing clinical samples.  ...  Yadav is the group leader for the Maximum Containment Laboratory, National Institute of Virology, Pune, India.  ... 
doi:10.3201/eid2405.171844 pmid:29664366 pmcid:PMC5938759 fatcat:uq45j34qurfgpmd7mkuqrk4jxi

miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy

Alexander S. Baras, Christopher J. Mitchell, Jason R. Myers, Simone Gupta, Lien-Chun Weng, John M. Ashton, Toby C. Cornish, Akhilesh Pandey, Marc K. Halushka, Wei Yan
2015 PLoS ONE  
In a head-to-head comparison with other miRNA analysis tools (miRExpress 2.0, sRNAbench, omiRAs, miRDeep2, Chimira, UEA small RNA Workbench), miRge was faster (4 to 32-fold) and was among the top-two methods  ...  Small RNA RNA-seq for microRNAs (miRNAs) is a rapidly developing field where opportunities still exist to create better bioinformatics tools to process these large datasets and generate new, useful analyses  ...  Acknowledgments The authors thank Igor Dolgalev for troubleshooting and helpful comments on developing the installation guidelines. Author Contributions  ... 
doi:10.1371/journal.pone.0143066 pmid:26571139 pmcid:PMC4646525 fatcat:grn2khpwunfjhjguougp6f4zga

Detection of Bovine Group A Rotavirus Using Rapid Antigen Detection Kits, RT-PCR and Next-Generation DNA Sequencing

Fujiko MINAMI-FUKUDA, Makoto NAGAI, Hikaru TAKAI, Toshiaki MURAKAMI, Tadashi OZAWA, Shinobu TSUCHIAKA, Sachiko OKAZAKI, Yukie KATAYAMA, Mami OBA, Naomi NISHIURA, Yukiko SASSA, Tsutomu OMATSU (+7 others)
2013 Journal of Veterinary Medical Science  
We investigated the sensitivity of human rotavirus rapid antigen detection (RAD) kits, RT-PCR and next-generation DNA sequencing (NGS) for detection of bovine group A rotavirus (RVA).  ...  The NGS would be sensitive and useful for analysis of less dependent on specific primers and screening of genotypes.  ...  This work was supported by a Grant-in-Aid for Research on Emerging and Re-emerging Infectious Diseases from the Ministry of Health, Labour and Welfare, Japan (grant H24-shinkou-ippan-005).  ... 
doi:10.1292/jvms.13-0265 pmid:23912876 pmcid:PMC3942952 fatcat:hsmmgmczsraw3lm4ojodr7fvoe

Use of S1 nuclease in deep sequencing for detection of double-stranded RNA viruses

Saya SHIMADA, Makoto NAGAI, Hiromitsu MORIYAMA, Toshiyuki FUKUHARA, Satoshi KOYAMA, Tsutomu OMATSU, Tetsuya FURUYA, Junsuke SHIRAI, Tetsuya MIZUTANI
2015 Journal of Veterinary Medical Science  
Metagenomic approach using next-generation DNA sequencing has facilitated the detection of many pathogenic viruses from fecal samples.  ...  Here, to improve efficiency of the detection of double-stranded (ds) RNA viruses from samples, we evaluated the applicability of S1 nuclease on deep sequencing.  ...  This study was supported by the Research Project for Improving Food Safety and Animal Health of the Ministry of Agriculture, Forestry and Fisheries of Japan.  ... 
doi:10.1292/jvms.14-0607 pmid:25843154 pmcid:PMC4591160 fatcat:26um5fxr3zgvrooenytk5zqona

Applied shotgun metagenomics approach for the genetic characterization of dengue viruses

Erley Lizarazo, Natacha Couto, Maria Vincenti-Gonzalez, Erwin C. Raangs, Zoraida Velasco, Sarah Bethencourt, Thomas Jaenisch, Alexander W. Friedrich, Adriana Tami, John W. Rossen
2019 Journal of Biotechnology: X  
Viral RNA was isolated with or without DNase-I treatment from 17 DENV (1-4) positive blood samples. cDNA libraries were generated using either a combination of the NEBNext® RNA to synthesize cDNA followed  ...  by Nextera XT DNA library preparation, or the TruSeq RNA V2 (TS) library preparation kit.  ...  We thank Maria Guadalupe Guzman for her valuable support in the performance of molecular detection of part of the samples.  ... 
doi:10.1016/j.btecx.2019.100009 pmid:34112375 fatcat:xco4xmqg4bh55aapuennunpoiu

An improved protocol for small RNA library construction using High Definition adapters

Ping Xu, Martina Billmeier, Irina Mohorianu, Darrell Green, William D Fraser, Tamas Dalmay
2015 Methods in Next Generation Sequencing  
Next generation sequencing of small RNA (sRNA) libraries is widely used for studying sRNAs in various biological systems.  ...  Here, we report a protocol to generate sRNA libraries using HD adapters with greatly reduced proportion of adapter-adapter products due to the degradation of nonligated 3' adapters.  ...  Acknowledgement: The work was funded by a BBSRC Sparking Impact Award granted by the University of East Anglia to Tamas Dalmay.  ... 
doi:10.1515/mngs-2015-0001 fatcat:7mwkxi4rh5h3xap7y3wby6ok4a

Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls

Anja Kovanda, Lea Leonardis, Janez Zidar, Blaž Koritnik, Leja Dolenc-Groselj, Stanislava Ristic Kovacic, Tomaž Curk, Boris Rogelj
2018 Scientific Reports  
Following small RNA-Seq, we compared the expression of small RNAs in muscle tissue of ALS patients and healthy age-matched controls.  ...  The identified snoRNAs, mtRNAs and other small RNAs provide possible molecular links between insulin signaling and ALS.  ...  Acknowledgements We would like to profoundly thank all the patients and controls for participating in the study.  ... 
doi:10.1038/s41598-018-23139-2 pmid:29618798 pmcid:PMC5884852 fatcat:7gov5ct7g5hefhtnnpivdo3sze

Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements

Ilektra-Chara Giassa, Panagiotis Alexiou
2021 Biology  
analysis through bisulfite sequencing data.  ...  Advancements in bioinformatics and machine learning approaches are increasingly contributing to the analysis of the regulation mechanisms.  ...  -C.G. and P.A. would like to thank Eva Klimentová for her help with the initial literature research for the bioinformatics tools. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biology10090896 pmid:34571773 pmcid:PMC8465862 fatcat:5a5osyvzfjhc3jogue42lgrtyy
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