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Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines

Anthony Federico, Tanya Karagiannis, Kritika Karri, Dileep Kishore, Yusuke Koga, Joshua D. Campbell, Stefano Monti
2019 Frontiers in Genetics  
This report highlights the design methodology behind Pipeliner that enables the development of highly flexible and reproducible pipelines that are easy to extend and maintain on multiple computing environments  ...  We have used Pipeliner to create several pipelines for sequencing data processing including bulk RNA-sequencing (RNA-seq), single-cell RNA-seq, as well as digital gene expression data.  ...  The scRNA-seq and DGE pipelines adopt a similar methodology, and the development of additional pipelines for microRNAseq (miRNA-seq) and RNA-seq Variant Calling is currently underway.  ... 
doi:10.3389/fgene.2019.00614 pmid:31316552 pmcid:PMC6609566 fatcat:pu7zj263tncifknlxiip4dwdqy

Utility of RNA Sequencing Analysis in the Context of Genetic Testing

Jackie Tahiliani, Jeanne Leisk, Kerry Aradhya, Karen Ouyang, Swaroop Aradhya, Keith Nykamp
2020 Current Genetic Medicine Reports  
Purpose of Review RNA analysis is beginning to be integrated into clinical laboratory genomics, and a review of its current uses and limitations is warranted.  ...  Summary RNA analysis is an important complement to DNA testing, although limitations still exist.  ...  This underscores the importance of carefully establishing the validity, reliability, and reproducibility of all RNA-seq methodologies before using evidence from RNA analysis to classify splice-site variants  ... 
doi:10.1007/s40142-020-00195-7 fatcat:v6qqp4zvwja2peqehmg743o4xi

Comprehensive molecular screening: from the RT-PCR to the RNA-seq

Carlota Costa, Ana Giménez-Capitán, Niki Karachaliou, Rafael Rosell
2013 Translational Lung Cancer Research  
However, this RNA-Seq technique will not likely replace current RT-PCR methods, but will be complementary depending on the needs and the resources of the clinic and the laboratory as the results of the  ...  RNA-Seq will identify those genes that need to then be examined using RT-PCR methods.  ...  However, this RNA-Seq technique will not likely replace current RT-PCR methods, but will be complementary ( Table 1 ).  ... 
doi:10.3978/j.issn.2218-6751.2013.02.05 pmid:25806219 pmcid:PMC4369859 fatcat:jcawzhwalveqzppsbjouqhm24e

A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups

Sheenah M. Mische, Nancy C. Fisher, Susan M. Meyn, Katia Sol Church, Rebecca L. Hegstad-Davies, Frances Weis-Garcia, Marie Adams, John M. Ashton, Kym M. Delventhal, Julie A. Dragon, Laura Holmes, Pratik Jagtap (+5 others)
2020 Journal of Biomolecular Techniques  
Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications.  ...  They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and thedy have institutional responsibility for the conduct  ...  to ensure the reporting of key methodological, and analytical information to reviewers and readers. 16, 19, 20 ACKNOWLEDGMENTS , 101 This RNA profiling phase of the ABRF-NGS Study included the Illumina  ... 
doi:10.7171/jbt.20-3101-003 pmid:31969795 pmcid:PMC6959150 fatcat:q5gkeiwsq5cy3fnitsh27hskde

High-throughput profiling for discovery of non-coding RNA biomarkers of lung disease

Paul J. McKiernan, Catherine M. Greene
2015 Expert Review of Molecular Diagnostics  
Non-coding RNA is expressed in all human cells: two major classes, ncRNA and microRNA, are detectable extracellularly in the circulation and other biofluids.  ...  This article presents and compares existing platforms for detection and quantification of ncRNA, specifically hybridization, qRT-PCR and RNA sequencing, and outlines methods for data interpretation and  ...  Each biofluid has characteristics that can affect non-coding RNA detection.  Accuracy, reliability and reproducibility of the methodologies are tantamount within this field.  ... 
doi:10.1586/14737159.2016.1122526 pmid:26581119 fatcat:2ngcmgeojjfvrlavi6bhw7twja

Urgent need for consistent standards in functional enrichment analysis

Kaumadi Wijesooriya, Sameer A. Jadaan, Kaushalya L. Perera, Tanuveer Kaur, Mark Ziemann, Melissa L. Kemp
2022 PLoS Computational Biology  
Using seven independent RNA-seq datasets, we show misuse of enrichment tools alters results substantially.  ...  These problems include the use of inappropriate background gene lists, lack of false discovery rate correction and lack of methodological detail.  ...  articles (Fig 2K ), limiting reproducibility.  ... 
doi:10.1371/journal.pcbi.1009935 pmid:35263338 pmcid:PMC8936487 fatcat:p7sr2qjf7nfllgpdxhmmjig3mm

RNA sequencing: advances, challenges and opportunities

Fatih Ozsolak, Patrice M. Milos
2010 Nature reviews genetics  
As noted above, most current RNA-seq methods rely on cDNA synthesis and a range of subsequent manipulation steps, which places limitations on the current approaches for some applications.  ...  The limitations of current RNA-seq approaches discussed above might be at least partly alleviated by emerging RNA analysis technologies, including DRS, that substantially alter the method of RNA characterization  ... 
doi:10.1038/nrg2934 pmid:21191423 pmcid:PMC3031867 fatcat:bo66nkxyb5dujdtuvnkgtsgpdu

Transcriptome-wide measurement of plant RNA secondary structure

Shawn W Foley, Lee E Vandivier, Pavel P Kuksa, Brian D Gregory
2015 Current opinion in plant biology  
We note hurdles to reliably measuring secondary structure, including RNA-binding proteins, RNA base modifications, and intramolecular duplexes.  ...  .: Transcriptome-wide measurement of plant RNA secondary structure, Curr Opin Plant Biol (2015), http://dx. RNAs fold into intricate and precise secondary structures.  ...  2 ( 2 RNA modifications and limitations to Structure-seq.  ... 
doi:10.1016/j.pbi.2015.05.021 pmid:26119389 pmcid:PMC5096376 fatcat:pxxs6mlrbzg6lefuqhj2n6pwpe

New Twists in Detecting mRNA Modification Dynamics

Ina Anreiter, Quoseena Mir, Jared T. Simpson, Sarath C. Janga, Matthias Soller
2020 Trends in Biotechnology  
Single-molecule sequencing introduced by Oxford Nanopore now promises to overcome such limitations, and we summarize current progress with a particular focus on the bioinformatic challenges of this novel  ...  The low abundance of nucleotide modifications and technical limitations, however, have hampered systematic analysis of their occurrence and functions.  ...  Acknowledgments We apologize to colleagues whose work was not cited owing to space limitations. We thank I. Haussmann and R. Arnold for comments on the manuscript. We thank R. Koonchanok  ... 
doi:10.1016/j.tibtech.2020.06.002 pmid:32620324 pmcid:PMC7326690 fatcat:op6u2lxbuzalfhposi5dnryhmi

Whole-Transcriptome Profiling on Small FFPE Samples: Which Sequencing Kit Should Be Used?

Marc Hilmi, Lucile Armenoult, Mira Ayadi, Rémy Nicolle
2022 Current Issues in Molecular Biology  
RNA sequencing (RNA-Seq) appears as a great tool with huge clinical potential, particularly in oncology.  ...  Overall, our results suggest that the Smarter is the most robust RNA-Seq technique to study small FFPE samples and 3′ Lexogen presents an interesting quality–price ratio for samples with less limiting  ...  total RNA-seq kit v3-pico (Smarter), and TECAN's Ovation SoLo (Solovation) RNA-Seq library preparation kit.  ... 
doi:10.3390/cimb44050148 fatcat:mvbh6nay6vcrfbrnixfvv7ornq

Butter: High-precision genomic alignment of small RNA-seq data [article]

Michael J Axtell
2014 bioRxiv   pre-print
These RNAs can be discovered, annotated, and quantified using small RNA-seq, a variant RNA-seq method based on highly parallel sequencing.  ...  Butter displays superior performance relative to other small RNA-seq aligners.  ...  Genomic alignment of small RNA-seq data is thus a critical methodology for the study of small RNAs.  ... 
doi:10.1101/007427 fatcat:42k6piwdhbg7vgjh47vgszsmoq

Efficient Production of On-Target Reads for Small RNA Sequencing of Single Cells Using Modified Adapters

Ruba Khnouf, Sabrina Shore, Crystal M. Han, Jordana M. Henderson, Sarah A. Munro, Anton P. McCaffrey, Hirofumi Shintaku, Juan G. Santiago
2018 Analytical Chemistry  
Although single-cell mRNA sequencing has been a powerful tool to explore cellular heterogeneity, the sequencing of small RNA at the single-cell level (sc-sRNA-seq) remains a challenge, as these have no  ...  We present two methods of single-cell-lysis that enable sc-sRNA-seq.  ...  An important exception to these advances in scRNA-seq, and the main focus of the current work, is the processing, isolation, and deep sequencing of small RNA (sRNA-seq) of single cells.  ... 
doi:10.1021/acs.analchem.8b02773 pmid:30260208 pmcid:PMC6233959 fatcat:r2smz3ack5fprl3fhsikjgg5yq

Analytical and Clinical Validation of Expressed Variants and Fusions From the Whole Transcriptome of Thyroid FNA Samples

Trevor E. Angell, Lori J. Wirth, Maria E. Cabanillas, Maisie L. Shindo, Edmund S. Cibas, Joshua E. Babiarz, Yangyang Hao, Su Yeon Kim, P. Sean Walsh, Jing Huang, Richard T. Kloos, Giulia C. Kennedy (+1 others)
2019 Frontiers in Endocrinology  
Methods: DNA and RNA were purified from the same sample across 943 blinded FNAs and compared by multiple methodologies, including whole-transcriptome RNA-seq, targeted RNA-seq, and targeted DNA-seq.  ...  Analytical Validation Shows the Variant and Fusion Calls Are Highly Reproducible Across Labs and Reagent Lots To determine the reproducibility of the whole-transcriptome RNA-seq assay across laboratories  ...  DATA AVAILABILITY Restrictions apply to the datasets: The datasets for this manuscript are not publicly available because the dataset and the research methodologies are proprietary.  ... 
doi:10.3389/fendo.2019.00612 fatcat:uslc2n6n25g5zfo4hyhm3g6dpe

Toxicogenomics: A 2020 Vision

Zhichao Liu, Ruili Huang, Ruth Roberts, Weida Tong
2019 TIPS - Trends in Pharmacological Sciences  
The RNA-Seq outperformed microarray due to low-abundance transcripts, which means the similar performance could be generated from both RNA-Seq and microarray platform when limiting the DEGs in the high  ...  Some novel genomics technologies such as RNA-Seq and TempO-Seq TM have been well established in the TGx field.  ... 
doi:10.1016/j.tips.2018.12.001 fatcat:bzqazo7oenhavkon7u6qn4zh4e

Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data

Sascha Jung, Vladimir Espinosa Angarica, Miguel A. Andrade-Navarro, Noel J. Buckley, Antonio del Sol
2017 Scientific Reports  
Different experimental procedures have been developed to obtain insights into the accessible chromatin landscape including DNase-seq, FAIRE-seq and ATAC-seq.  ...  this study also proved that the selection of the parameters used by each peak-caller has significant effects on the genome wide Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts  ...  FAIRE-seq or DNase-seq -suffer from different inherent limitations.  ... 
doi:10.1038/s41598-017-04929-6 pmid:28680085 pmcid:PMC5498635 fatcat:a55xaur2frgbtoxny4lyxphiz4
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