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Metrics for rapid quality control in RNA structure probing experiments
2016
Bioinformatics
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The developed metrics and tools will be useful in summarizing large-scale datasets and will help standardize quality control in the field. ...
General and efficient methodologies are needed to quantify variability and quality in the wide range of current and emerging structure probing experiments. ...
Acknowledgement We thank Yun Bai for providing us with SHAPE-Seq data for HIV-1 RRE.
Funding ...
doi:10.1093/bioinformatics/btw501
pmid:27497441
pmcid:PMC5181532
fatcat:zhqzigjr2nd4tbyzvjze24g76q
Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA
2007
BMC Biotechnology
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In contrast, thawing of tissue led to a rapid loss of RNA integrity. ...
Probe sets identified as most sensitive to RNA degradation tended to be located more than 1000 nucleotides upstream of their transcription termini, similar to the positioning of control probe sets used ...
RNA degradation was much more rapid in frozen tissue. Poor quality RNA (RIN ≤ 7) was isolated from frozen tissue thawed for 15-30 min at room temperature. ...
doi:10.1186/1472-6750-7-57
pmid:17854504
pmcid:PMC2082023
fatcat:4kmtddkt2bfq7jitbokwgurafm
Turbo FISH: A Method for Rapid Single Molecule RNA FISH
2013
PLoS ONE
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Citation: Shaffer SM, Wu M-T, Levesque MJ, Raj A (2013) Turbo FISH: A Method for Rapid Single Molecule RNA FISH. PLoS ONE 8(9): e75120. ...
Advances in RNA fluorescence in situ hybridization (RNA FISH) have allowed practitioners to detect individual RNA molecules in single cells via fluorescence microscopy, enabling highly accurate and sensitive ...
Cook) for providing reagents used in the Turbo FISH assay; the lab of P. Sharp (Massachusetts Institute of Technology) for providing the HeLa cells; and the lab of M. ...
doi:10.1371/journal.pone.0075120
pmid:24066168
pmcid:PMC3774626
fatcat:wef23mtq3jcdtfq6n3pd6nkj3i
Data quality in genomics and microarrays
2006
Nature Biotechnology
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To date, the MicroArray Quality Control (MAQC) project-the first results of which are presented in this issue-and the External RNA Controls Consortium (ERCC) are the most comprehensive efforts in assessing ...
Currently, few if any objective metrics or established quality control standards are used to evaluate the quality of microarray studies. ...
Building in a quality control assessment and an incorporated report of quality metrics would be enormously useful in a variety of settings (Fig. 1) . ...
doi:10.1038/nbt0906-1112
pmid:16964224
pmcid:PMC2943412
fatcat:35hkslbwobf5pck434jftodygq
Review Article: Current Knowledge on Microarray Technology - An Overview
2012
Tropical Journal of Pharmaceutical Research
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The completion of whole genome sequencing projects has led to a rapid increase in the availability of genetic information. ...
In the field of transcriptomics, the emergence of microarray-based technologies and the design of DNA biochips allow high-throughput studies of RNA expression in cell and tissue at a given moment. ...
ERCC (External RNA Control Consortium), The Norwegian Microarray Consortiums (NMC) and MAQC (Microarray Quality Control) project are some of the groups which aim to provide quality control (QC) tools to ...
doi:10.4314/tjpr.v11i1.20
fatcat:mmcib73d3jb2flm4fx4lqhcq2a
Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline
2014
Cancer Informatics
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QuaCRS (Quality Control for RNA-Seq) is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and ...
The structure of the QuaCRS database is designed to enable expansion with additional tools and metrics in the future. ...
David Lucas, Department of Internal Medicine, for his assistance in this manuscript.
Author contributions ...
doi:10.4137/cin.s14022
pmid:25368506
pmcid:PMC4214596
fatcat:yedm4z42ebhw3paaqoxzko3riu
Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions
2017
Quantitative Biology
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Structure profiling experiments provide single-nucleotide information on RNA structure. ...
Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transcriptome scale and in living cells, creating unprecedented opportunities for ...
Counts from experiment and control assays are then combined to obtain reactivity profiles for all RNAs in the sample. ...
doi:10.1007/s40484-017-0093-6
pmid:28717530
pmcid:PMC5510538
fatcat:cuuzemscpjagrdvfczdwbtwenq
Trends and challenges in computational RNA biology
2016
Genome Biology
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Acknowledgements We thank Sander Granneman, Grzegorz Kudla, Edward Wallace and the conference organisers for critically reading the manuscript. ...
the UK Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council and Medical Research Council to the University of Edinburgh Doctoral Training Centre in ...
In poster sessions, Krishna Choudhary (University of California, Davis, USA) highlighted the importance of quality control by presenting metrics for rapid quality assessment of structure probing data. ...
doi:10.1186/s13059-016-1117-7
pmid:27927225
pmcid:PMC5141647
fatcat:5jctjbmzfnaqtlud4ehxgxhyde
Platinum Sponsor Talk: New Options for Methylome Analysis and RNA Depletion
2019
Journal of Biomolecular Techniques
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For applications where the full spectrum of RNA is of interest or where poly(A) tails are not present, a method for depletion of abundant RNAs is required. ...
Probe sets for the NEBNext RNaseH-based depletion method are being expanded to remove adult, fetal and embryonic hemoglobin transcripts from blood samples (in which globin can constitute up to ∼60% of ...
Europe) networks have drafted guidelines for improved quality control (QC). ...
pmid:31897020
pmcid:PMC6938120
fatcat:wxy7ayk37zfjzezwn2oy3fepka
Power enhancement via multivariate outlier testing with gene expression arrays
2008
Bioinformatics
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Funding: Subcontract from the Immune Tolerance Network; a project of the National Institute of Allergy and Infectious Diseases; The National Institute for Diabetes, Digestive and Kidney Diseases; Juvenile ...
For positive controls, ...
There is no basis at present for objective choice of base quality metrics, for the choice of number of principal components to use in reduction, or for the choice of null outlier labeling rate α that will ...
doi:10.1093/bioinformatics/btn591
pmid:19015138
pmcid:PMC2638936
fatcat:2hetq63zf5dc5otxppyhbdh5cu
Flow-dependent regulation of genome-wide mRNA and microRNA expression in endothelial cells in vivo
2014
Scientific Data
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We also developed a novel method to collect endothelial-enriched RNAs from the carotids of these animals, which enabled us to perform genome-wide expression analyses of mRNAs and miRNAs in the arterial ...
developed a mouse model of atherosclerosis that rapidly develops robust atherosclerosis by partially ligating the left carotid artery (LCA) branches, while using the contralateral right carotid (RCA) as control ...
., originally published in 2009 and 2013 in the Journals Blood 2 and Nature Communications 11 , respectively. ...
doi:10.1038/sdata.2014.39
pmid:25977794
pmcid:PMC4411008
fatcat:lz3wrknp6jhkfbxxm7bw5yrq3a
Optimised laser microdissection of the human ocular surface epithelial regions for microarray studies
2013
BMC Ophthalmology
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To achieve the desired RNA concentration the area of ocular surface epithelial tissue sample processed for the Gene 1.0 ST array experiments was approximately 100,0000 μm 2 to 130,0000 μm 2 . ...
The area of LMD tissue processed for spotted oligonucleotide microarray study ranged from 86,253 μm 2 in LEC to 392,887 μm 2 in LEC stroma. ...
Figure 6 6 Composite image of Quality Control metrics applied in Gene 1.0 ST array. Image A is of an Agilent assay of a RNA sample showing two peaks 18S and 28S of ribosomal RNA. ...
doi:10.1186/1471-2415-13-62
pmid:24160452
pmcid:PMC4015997
fatcat:krfi6utb3jhr3ivpadftk5yrea
Technology Development to Explore the Relationship Between Oral Health and the Oral Microbial Community
2006
BMC Oral Health
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This review addresses a core technology using gel-based microarrays and the initial integration of this technology into a single device needed for system-wide studies of complex microbial community structure ...
and for the development of oral diagnostic devices. ...
Without quality controls, for example by adding a control probe labeled with the same fluorophore as the target in the gel array, it is difficult to deconvolute these two processes. ...
doi:10.1186/1472-6831-6-s1-s10
pmid:16934111
pmcid:PMC2147590
fatcat:ntvf63eaxfdwpjorybl6icevce
Improving the analysis of quantitative PCR data in veterinary research
2012
The Veterinary Journal
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Very few veterinary publications provide information on RNA quality and integrity and there is little information on the reverse transcription step or on the efficiency of the subsequent PCR. ...
The so-called 'Minimum Information for publication of Quantitative real-time PCR Experiments' (MIQE) guidelines aim to improve the standard of publications utilising qPCR by providing a checklist of the ...
These use quality metrics, such as the RNA integrity number (RIN; Agilent), RNA quality indicator (RQI; BioRad) or Screen-Tape degradation value (SDV; Lab901) to represent the level of degradation in a ...
doi:10.1016/j.tvjl.2011.06.044
pmid:22005167
fatcat:s2enrwbdwjejvdrmhkpsqp3os4
GPR-Analyzer: a simple tool for quantitative analysis of hierarchical multispecies microarrays
2012
Environmental science and pollution research international
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In addition, normalized total signal intensities are recommended for comparisons between microarrays and in order to relate signals for specific probes to cell concentrations using external calibration ...
to identify potential false-positives considering parallel and hierarchical probes. ...
Linda K Medlin and Jessica Kegel provided the hierarchy file used as a basis for the file included in the GPR-Analyzer package. ...
doi:10.1007/s11356-012-1051-5
pmid:22767354
fatcat:a5uav2izsbdvffo6owssnjgemm
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