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Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression

Michele A. Busby, Chip Stewart, Chase A. Miller, Krzysztof R. Grzeda, Gabor T. Marth
2013 Computer applications in the biosciences : CABIOS  
Motivation: A common question arises at the beginning of every experiment where RNA-Seq is used to detect differential gene expression between two conditions: How many reads should we sequence?  ...  Results: Scotty is an interactive web-based application that assists biologists to design an experiment with an appropriate sample size and read depth to satisfy the user-defined experimental objectives  ...  ACKNOWLEDGEMENTS We thank our system administrator Tony Schreiner for substantial help in deploying Scotty on the web and Kourosh Zarringhalam, Patricia Smith, and Igor Lasic for helpful suggestions.  ... 
doi:10.1093/bioinformatics/btt015 pmid:23314327 pmcid:PMC3582267 fatcat:p4tygpyg3ngudomueihcctsfhm

RNAtor: an Android-based application for biologists to plan RNA sequencing experiments

Shruti Kane, Himanshu Garg, Neeraja M. Krishnan, Aditya Singh, Binay Panda
2017 F1000Research  
.: Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. Bioinformatics. 2013; 29(5): 656-657.  ...  Thus, we developed , a mobile application for Android platforms, to aid RNAtor biologists in correctly designing their RNA-seq experiments.  ...  Web-based tools, Scotty (Busby et al., 2013) and EDDA (Luo et al., 2014) , have an established precedence in aiding RNA-seq design.  ... 
doi:10.12688/f1000research.11982.2 fatcat:cpcaxa63orfarbrbtszwv3dhbe

RNAtor: an Android-based application for biologists to plan RNA sequencing experiments

Shruti Kane, Himanshu Garg, Neeraja M. Krishnan, Aditya Singh, Binay Panda
2017 F1000Research  
.: Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. Bioinformatics. 2013; 29(5): 656-657.  ...  Thus, we developed , a mobile application for Android platforms, to aid biologists in correctly RNAtor designing their RNA-seq experiments.  ...  Scotty, a previously reported, useful, interactive web-based tool aids RNA-seq experimental design.  ... 
doi:10.12688/f1000research.11982.1 fatcat:sdq4zhbibzfwhkc5iqtb7h5pqa

RNAtor: an Android-based application for biologists to plan RNA sequencing experiments [article]

Shruti Kane, Himanshu Garg, Neeraja M Krishnan, Aditya Singh, Binay Panda
2016 bioRxiv   pre-print
Keeping this in mind, we have developed RNAtor, a mobile application for Android platforms, to aid biologists in correctly designing their RNA-seq experiments.  ...  RNA sequencing (RNA-seq) is a powerful technology for identification of novel transcripts (coding, non-coding and splice variants), understanding of transcript structures and estimation of gene and/or  ...  Near-optimal probabilistic RNA-seq quantification. , M.A., et al. Scotty: a web tool for designing RNA-Seq experiments to measure 133 differential gene expression.  ... 
doi:10.1101/095315 fatcat:2rtunz3xgrbzvcwipebw6xct74

Global transcriptomic changes occur in uterine fluid-derived extracellular vesicles during the endometrial window for embryo implantation

E Giacomini, G M Scotti, V S Vanni, D Lazarevic, S Makieva, L Privitera, S Signorelli, L Cantone, V Bollati, V Murdica, G Tonon, E Papaleo (+2 others)
2021 Human Reproduction  
Differential gene expression (DGE) analysis was used to compare RNA-seq results between different groups of samples.  ...  On the largest sample size of human EVs ever analyzed with RNA-seq, this study establishes a gene signature to use for less-invasive endometrial receptivity tests.  ...  Conflict of interest The authors have no financial and non-financial competing interests to disclose.  ... 
doi:10.1093/humrep/deab123 pmid:34190319 fatcat:fbb36opzx5fmrfrokhojrqrlya

Integration of transcriptomic and genomic data suggests candidate mechanisms for APOE4-mediated pathogenic action in Alzheimer's disease

Laura Caberlotto, Luca Marchetti, Mario Lauria, Marco Scotti, Silvia Parolo
2016 Scientific Reports  
Late onset AD is the most common form but, although several putative susceptibility genes have been reported, APOE, coding for the Apolipoprotein E, is the most robust susceptibility gene known to date  ...  APOE is a multifunctional glycosylated protein with a major role in lipid transport and atherosclerosis pathogenesis and it is expressed in several organs, with the highest expression in the liver and  ...  As such, the investigators within the ADNI contributed to the design and implementation of ADNI and/or provided data but did not participate in analysis or writing of this report.  ... 
doi:10.1038/srep32583 pmid:27585646 pmcid:PMC5009326 fatcat:vlw4pdwcgrf7rd24kyvo2bxkf4

RNA-Sequencing: A tool to explore new frontiers in animal genetics

Saumya Wickramasinghe, Angela Cánovas, Gonzalo Rincón, Juan F. Medrano
2014 Livestock Science  
Recently, RNA-Seq technology has increasingly been used in livestock, wild and aquatic animal studies to measure gene expression analysis and SNP discovery.  ...  Global gene expression profiling by RNA-Sequencing (RNA-Seq) was introduced in 2004 with the advent of next generation sequencing technologies and has made a revolutionary impact on transcriptome analysis  ...  A. Cánovas was supported by a postdoctoral grant from ME/Fulbright.  ... 
doi:10.1016/j.livsci.2014.06.015 fatcat:hrqcthhvkjefvkpect7ygw6lx4

Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

Rebekah A. Oomen, Jeffrey A. Hutchings, Kristi M. Miller
2017 Facets  
The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature.  ...  Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by  ...  Author contributions Conceived and designed the study: RAO, JAH. Performed the experiments/collected the data: RAO. Analyzed and interpreted the data: RAO. Drafted or revised the manuscript: RAO, JAH.  ... 
doi:10.1139/facets-2017-0015 fatcat:gl7pac2onfetfalhvbbah5i4ja

Comprehensive multi-omics analysis uncovers a group of TGF-β-regulated genes among lncRNA EPR direct transcriptional targets

Ettore Zapparoli, Paola Briata, Martina Rossi, Lorenzo Brondolo, Gabriele Bucci, Roberto Gherzi
2020 Nucleic Acids Research  
Long non-coding RNAs (lncRNAs) can affect multiple layers of gene expression to control crucial cellular functions.  ...  Finally, we integrated data derived from ChIRP-Seq, ChIP-Seq as well as RNA-Seq in a comprehensive analysis and we selected a group of bona fide direct transcriptional targets of EPR.  ...  We are grateful to people at TIB Mol. Biol. (Genova branch) for their professional assistance and to Laura Marcenaro and Laura Miscioscia for excellent administrative work.  ... 
doi:10.1093/nar/gkaa628 pmid:32756918 fatcat:3s6zlkjqnzekhp5nc7q2ftuwpy

Long Noncoding RNA Discovery in Cardiovascular Disease

Tamer Sallam, Jaspreet Sandhu, Peter Tontonoz
2018 Circulation Research  
The recent identification of a fascinating group of mediators known as long noncoding RNAs (lncRNAs) has provided a wealth of new biology to explore for cardiovascular risk mitigation. lncRNAs are expressed  ...  In this review, we provide a road map for lncRNA discovery and interrogation in biological systems relevant to cardiovascular disease and highlight approaches to decipher their modes of action.  ...  Acknowledgments We apologize to many of our colleagues whose work was not included because of space constraints.  ... 
doi:10.1161/circresaha.117.311802 pmid:29301847 pmcid:PMC5902384 fatcat:dkibfeg535bppgh3uhxxygoxy4

Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model

Kathy A. Schall, Matthew E. Thornton, Mubina Isani, Kathleen A. Holoyda, Xiaogang Hou, Ching-Ling Lien, Brendan H. Grubbs, Tracy C. Grikscheit
2017 BMC Genomics  
Results: RNA-seq analysis identified 1346 significantly upregulated genes and 678 significantly downregulated genes in SBS zebrafish intestine compared to sham with Ingenuity analysis.  ...  RT-qPCR confirmed gene expression differences from RNA-Sequencing.  ...  Results After 2 weeks of SBS, zebrafish intestine has a high number of upregulated differentially expressed genes based on RNA sequencing Correlating with multiple previous experiments in this model, and  ... 
doi:10.1186/s12864-016-3433-4 pmid:28118819 pmcid:PMC5264326 fatcat:2h2izftnazggtpaoqbd7o2trle

Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ

C. W. Resnyk, W. Carré, X. Wang, T. E. Porter, J. Simon, E. Le Bihan-Duval, M. J. Duclos, S. E. Aggrey, L. A. Cogburn
2017 BMC Genomics  
The RNA sequencing analysis identified 2410 differentially expressed genes in abdominal fat of HG versus LG chickens at 7 wk.  ...  Results: Time-course microarray analysis revealed 312 differentially expressed genes (FDR ≤ 0.05) as the main effect of genotype (HG versus LG), 718 genes in the interaction of age and genotype, and 2918  ...  Acknowledgements The longitudinal study and tissue sampling of the divergent lines required the contribution of a large number of scientists and technicians from the laboratories and breeding facilities  ... 
doi:10.1186/s12864-017-4035-5 pmid:28814270 pmcid:PMC5559791 fatcat:npsxt75wufhnpad6624rdvqrhi

Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice

Pabodha Hettige, Uzma Tahir, Kiisa C. Nishikawa, Matthew J. Gage
2020 BMC Genomics  
We demonstrate the power of this approach by comparing the differential gene expression patterns of extensor digitorum longus (EDL), psoas, and soleus from mice using high throughput RNA sequencing.  ...  Furthermore, significant expression differences between psoas and EDL were observed in genes coding for myosin light chain, troponin, tropomyosin isoforms, and several genes encoding the constituents of  ...  core research facilities for his kind support in data generation, and the computational resources from the University of Massachusetts Green High-Performance Computing Cluster (GHPCC).  ... 
doi:10.1186/s12864-020-07225-2 pmid:33213377 pmcid:PMC7678079 fatcat:fllocwibvzbvfjzj5z3lrix7lm

Effect of Monoacylglycerol Lipase Inhibition on Intestinal Permeability of Rats With Severe Acute Pancreatitis

Jing Wang, Hongwei Xu, Tianjie Chen, Changqin Xu, Xiaohua Zhang, Shule Zhao
2022 Frontiers in Pharmacology  
A total of 132 RNA-binding proteins (RBPs) were screened by crossing the identified abnormally expressed genes with the reported RBP genes.  ...  Among them, HNRNPDL coexpressed the most AS events as the main RBP.Conclusion: MAGL inhibition improved intestinal mucosal barrier injury in SAP rats and induced a large number of differentially expressed  ...  In house tool Sogen was utilized to view the RNA-seq data with gene structure and junction reads.  ... 
doi:10.3389/fphar.2022.869482 pmid:35496266 pmcid:PMC9039313 fatcat:6j5v5rhlvzhm5jkkui2c2x7qbm

Experimental Considerations for Single-Cell RNA Sequencing Approaches

Quy H. Nguyen, Nicholas Pervolarakis, Kevin Nee, Kai Kessenbrock
2018 Frontiers in Cell and Developmental Biology  
This study was supported by funds from the National Cancer Institute (R00 CA181490), Chan/Zuckerberg Initiative (HCA-A-1704-01668), and the University of California Cancer Research Coordinating Committee  ...  Several methods have been developed using power analysis statistics, such as Scotty 1 or web-based tools 2 , but one must estimate the number and expected frequencies of cell populations present in the  ...  Quality Control Due to the high cost of single-cell sequencing experiments, careful quality control measurements should be executed.  ... 
doi:10.3389/fcell.2018.00108 pmid:30234113 pmcid:PMC6131190 fatcat:ybd6fa5wbbenzemos7rfqt3dei
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