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Metrics for rapid quality control in RNA structure probing experiments

Krishna Choudhary, Nathan P. Shih, Fei Deng, Mirko Ledda, Bo Li, Sharon Aviran
2016 Bioinformatics  
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

Karol L Thompson, P Scott Pine, Barry A Rosenzweig, Yaron Turpaz, Jacques Retief
2007 BMC Biotechnology  
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

Sydney M. Shaffer, Min-Tzu Wu, Marshall J. Levesque, Arjun Raj, Domingos Henrique
2013 PLoS ONE  
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

Hanlee Ji, Ronald W Davis
2006 Nature Biotechnology  
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

CN Naidu, Y Suneetha
2012 Tropical Journal of Pharmaceutical Research  
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

Karl W. Kroll, Nima E. Mokaram, Alexander R. Pelletier, David E. Frankhouser, Maximillian S. Westphal, Paige A. Stump, Cameron L. Stump, Ralf Bundschuh, James S. Blachly, Pearlly Yan
2014 Cancer Informatics  
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

Krishna Choudhary, Fei Deng, Sharon Aviran
2017 Quantitative Biology  
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

Alina Selega, Guido Sanguinetti
2016 Genome Biology  
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

Fiona Stewart
2019 Journal of Biomolecular Techniques  
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

A. L. Asare, Z. Gao, V. J. Carey, R. Wang, V. Seyfert-Margolis
2008 Bioinformatics  
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

Sandeep Kumar, Chan Woo Kim, Dong Ju Son, Chih Wen Ni, Hanjoong Jo
2014 Scientific Data  
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

Bina B Kulkarni, Desmond G Powe, Andrew Hopkinson, Harminder S Dua
2013 BMC Ophthalmology  
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

E Michelle L Starke, James C Smoot, Laura M Smoot, Wen-Tso Liu, Darrell P Chandler, Hyun H Lee, David A Stahl
2006 BMC Oral Health  
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

Stephen Bustin, Louis C. Penning
2012 The Veterinary Journal  
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

Simon M. Dittami, Bente Edvardsen
2012 Environmental science and pollution research international  
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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