A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines
2019
Frontiers in Genetics
Preserved Fulltext
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
2020
Current Genetic Medicine Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2013
Translational Lung Cancer Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2020
Journal of Biomolecular Techniques
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2015
Expert Review of Molecular Diagnostics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2022
PLoS Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
2010
Nature reviews genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2015
Current opinion in plant biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2020
Trends in Biotechnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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?
2022
Current Issues in Molecular Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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]
2014
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2018
Analytical Chemistry
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2019
Frontiers in Endocrinology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2019
TIPS - Trends in Pharmacological Sciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2017
Scientific Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 7,555 results