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RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment

Yan Guo, Shilin Zhao, Chung-I Li, Quanhu Sheng, Yu Shyr
2014 Cancer Informatics  
Sample size and power calculation is required for applications for National Institutes of Health (NIH) funding.  ...  Recent developments in high-throughput sequencing technology have allowed RNAseq to replace microarray as the technology of choice for high-throughput gene expression profiling.  ...  Acknowledgement The authors thank Margot Bjoring for her editorial support.  ... 
doi:10.4137/cin.s17688 pmid:25374457 pmcid:PMC4213196 fatcat:iatllwtct5c5jb6qcgvnpmzqvm

Targeted DNA Methylation Analysis by High Throughput Sequencing in Porcine Peri-attachment Embryos

Benson H. MORRILL, Lindsay COX, Anika WARD, Sierra HEYWOOD, Randall S. PRATHER, S. Clay ISOM
2013 Journal of reproduction and development  
The purpose of this experiment was to implement and evaluate the effectiveness of a next-generation sequencing-based method for DNA methylation analysis in porcine embryonic samples.  ...  Resulting PCR products were subjected to high-throughput sequencing using the Illumina Genome Analyzer IIx platform. The average depth of sequencing coverage was 14,611 for IVV and 17,068 for PA.  ...  We also recognize Bill Spollen at the Informatics Research Core Facility (University of Missouri) and Jon Huppi of the Center for High Performance Computing (Utah State University) for their contributions  ... 
doi:10.1262/jrd.2012-144 pmid:23428632 pmcid:PMC3934139 fatcat:me4dgkgj4nb3bne2x7hco7i7mi

Small sample sizes in high-throughput miRNA screens: A common pitfall for the identification of miRNA biomarkers

M.G.M. Kok, M.W.J. de Ronde, P.D. Moerland, J.M. Ruijter, E.E. Creemers, S.J. Pinto-Sietsma
2018 Biomolecular Detection and Quantification  
However, nowadays the falling costs and high specificity of small RNA sequencing make NGS a more attractive tool for high-throughput screening.  ...  Independent of the method used for high throughput screening, this can lead erroneous study results of the experiment: the so-called small sample size error.  ... 
doi:10.1016/j.bdq.2017.11.002 pmid:29276692 pmcid:PMC5737945 fatcat:x7rmiujmfjfllkpyba53s5bwpq

A note on statistical repeatability and study design for high-throughput assays

George Nicholson, Chris Holmes
2016 Statistics in Medicine  
Characterizing the technical precision of measurements is a necessary stage in the planning of experiments and in the formal sample size calculation for optimal design.  ...  We present an alternative framework for assessing the precision of high-throughput assays and planning biomedical experiments.  ...  Acknowledgements The authors would like to thank Rory Bowden, Tristan Gray-Davies, Davis McCarthy, Matti Pirinen, Chris Spencer, Aimee Taylor, James Watson and Quin Wills for helpful comments on the paper  ... 
doi:10.1002/sim.7175 pmid:27882571 pmcid:PMC5299465 fatcat:svprk7xxuvgtrckb3timh3a7ya

COPAR: A ChIP-Seq Optimal Peak Analyzer

Binhua Tang, Xihan Wang, Victor X. Jin
2017 BioMed Research International  
It provides a versatile perspective for biologists to perform quality-check for high-throughput experiments and optimize their experiment design.  ...  The package COPAR can process mapped ChIP-seq read file in BED format and output statistically sound results for multiple high-throughput experiments.  ...  and statistically compare multiple ChIP-seq samples for NGS high-throughput experiments.  ... 
doi:10.1155/2017/5346793 pmid:28357402 pmcid:PMC5357551 fatcat:ahw7d6ogdbg47dopyagdtuhxhi

Fragmentation of pooled PCR products for highly multiplexed TILLING [article]

Andrea Tramontano, Luka Jarc, Joanna Jankowicz-Cieslak, Bernhard J. Hofinger, Katarzyna Gajek, Miriam Szurman-Zubrzycka, Iwona Szarejko, Ivan Inglebrecht, Bradley J. Till
2018 biorxiv/medrxiv   pre-print
Evaluation of read coverage and base quality across amplicons suggests this approach is suitable for high-throughput TILLING and other applications employing highly pooled complex sampling schemes.  ...  Using PCR to target and sequence chosen genomic regions provides an attractive alternative as the vast reduction in interrogated bases means that sample size can be dramatically increased through amplicon  ...  ACKNOWLEDGMENTS We thank Keji Dada of the Cocoa Research Institute of Nigeria for assistance in coffee primer design and testing. Professor Margit Laimer of BOKU provided Coffea arabica genomic DNA.  ... 
doi:10.1101/451567 fatcat:jmnookhlrvf2jninh7q6kmjjla

A Measurement Study for Predicting Throughput from LQI and RSSI [chapter]

Krzysztof Wolosz, Ulf Bodin, Laurynas Riliskis
2012 Lecture Notes in Computer Science  
Results include variability of throughput, RSSI and LQI observed for different transmission powers, transmission ranges, and number of transmitting nodes. we present the tested system and configuration  ...  settings used in the experiments, and system validation results.  ...  For such system we believe a cognitive and distributed scheduler to be a key component, making the system stable and predictable for communicating sensed data.  ... 
doi:10.1007/978-3-642-34976-8_10 fatcat:6x4fl7pqcnf6pdlewh4ajt3hxi

High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae

Vincent J. Fasanello, Ping Liu, Carlos A. Botero, Justin C. Fay
2020 PeerJ  
These findings demonstrate the utility of this new resource for designing and improving high-throughput studies of experimental evolution.  ...  The approach described here provides a framework for future studies employing experimental designs that require high-throughput multiplexed fitness measurements.  ...  Botero and Justin C. Fay labs, specifically Angela M. Chira, Trevor S. Fristoe, Emery Longan, and Dilys M. Vela Diaz for ongoing feedback and helpful advice.  ... 
doi:10.7717/peerj.10118 pmid:33088623 pmcid:PMC7571412 fatcat:256xzzhph5eonllgirzp2c2nvu

Fragmentation of Pooled PCR Products for Highly Multiplexed TILLING

Andrea Tramontano, Luka Jarc, Joanna Jankowicz-Cieslak, Bernhard J. Hofinger, Katarzyna Gajek, Miriam Szurman-Zubrzycka, Iwona Szarejko, Ivan Ingelbrecht, Bradley J. Till
2019 G3: Genes, Genomes, Genetics  
Evaluation of read coverage and base quality across amplicons suggests this approach is suitable for high-throughput TILLING and other applications employing highly pooled complex sampling schemes.  ...  Using PCR to target and sequence chosen genomic regions provides an attractive alternative as the vast reduction in interrogated bases means that sample size can be dramatically increased through amplicon  ...  ACKNOWLEDGMENTS We thank Keji Dada of the Cocoa Research Institute of Nigeria for assistance in coffee primer design and testing. Professor Margit Laimer of BOKU provided Coffea arabica genomic DNA.  ... 
doi:10.1534/g3.119.400301 pmid:31213514 pmcid:PMC6686939 fatcat:b7qxoarl5zeftnicwnb3355gjm

High-Throughput Massively Parallel Sequencing for Fetal Aneuploidy Detection from Maternal Plasma

Taylor J. Jensen, Tricia Zwiefelhofer, Roger C. Tim, Željko Džakula, Sung K. Kim, Amin R. Mazloom, Zhanyang Zhu, John Tynan, Tim Lu, Graham McLennan, Glenn E. Palomaki, Jacob A. Canick (+5 others)
2013 PLoS ONE  
Numerous research and clinical studies have described the analysis of ccf DNA using next generation sequencing for the detection of fetal aneuploidies with high sensitivity and specificity.  ...  Classification was based upon a standard normal transformed cutoff value of z = 3 for chromosome 21 and z = 3.95 for chromosomes 18 and 13.  ...  Author Contributions Conceived and designed the experiments: PO CD DvdB ME GEP JAC. Performed the experiments: TJJ TZ RCT JT. Analyzed the data: TJJ ZD SKK ARM ZZ TL CD ME.  ... 
doi:10.1371/journal.pone.0057381 pmid:23483908 pmcid:PMC3590217 fatcat:s4kcwqa3p5fiblnn2i3gkleq6a

PROPER: comprehensive power evaluation for differential expression using RNA-seq

Hao Wu, Chi Wang, Zhijin Wu
2014 Computer applications in the biosciences : CABIOS  
The complexity and flexibility of RNA-seq experiments, the high-throughput nature of transcriptome-wide expression measurements and the unique characteristics of RNA-seq data make the power assessment  ...  Results: We propose prospective power assessment instead of a direct sample size calculation by making assumptions on all of these factors.  ...  Power reassessment One challenge in the sample size determination in high-throughput experiment is the choice of type I error control.  ... 
doi:10.1093/bioinformatics/btu640 pmid:25273110 pmcid:PMC4287952 fatcat:5goycrvg45ezpon6e7ztlv2ohq

Improved Performance of SRAM-Based True Random Number Generator by Leveraging Irradiation Exposure

Xu Zhang, Chunsheng Jiang, Gang Dai, Le Zhong, Wen Fang, Ke Gu, Guoping Xiao, Shangqing Ren, Xin Liu, Sanyong Zou
2020 Sensors  
., randomness and throughput) improvement method of SRAM-based TRNG is proposed, and its implementation can be divided into two phases: irradiation exposure and hardware postprocessing.  ...  Additionally, while the data remanence effect hampers obtaining random bitstreams with high speed, the ionization irradiation can also weaken this impact and improve the throughput of TRNG.  ...  The min-entropy of every bit (bit i ) in the SRAM power-on sequence can be calculated by Equations (1) and (2) .  ... 
doi:10.3390/s20216132 pmid:33126596 fatcat:mgom2r46n5aibdg2nyhoxfmabu

An experimental study on performance comparison of rate adaptation and fixed rate in IEEE 802.11g

Dong Xia, Qiang Fu
2011 2011 Australasian Telecommunication Networks and Applications Conference (ATNAC)  
Qiang Fu for the continuous help and support of my master study and research, for his patience, motivation, enthusiasm, and immense knowledge.  ...  In the last few years, we have seen that the demand for high-bandwidth wireless local area networks increases rapidly, due to the proliferation of mobile devices such as laptops, smart phones and tablet  ...  Retransmission counter and throughput for each data rate is calculated based on an ideal transmission time for each rate.  ... 
doi:10.1109/atnac.2011.6096661 dblp:conf/itnac/XiaF11 fatcat:hz6qgkma7nexflayoedb7zboja

A Highly-Accurate and Low-Overhead Prediction Model for Transfer Throughput Optimization

JangYoung Kim, Esma Yildirim, Tevfik Kosar
2012 2012 SC Companion: High Performance Computing, Networking Storage and Analysis  
To alleviate this bottleneck, we propose an application-layer throughput optimization model based on parallel stream number prediction.  ...  We test and compare these four models on emulated testbeds as well as on production environments using a wide variety of data set sizes, RTT, and bandwidth combinations.  ...  ACKNOWLEDGMENT This project is partially supported by NSF under award numbers CNS-1131889 (CAREER), OCI-0926701 (STCI-Stork), and CCF-1115805 (CiC-Stork).  ... 
doi:10.1109/sc.companion.2012.109 dblp:conf/sc/KimYK12 fatcat:vvtj6rjuljdkfnnyfgvfaofrm4

Analysis of Pel Decimation and Technology Choices to Reduce Energy on SAD Calculation

Ismael Seidel, André Beims Bräscher, Bruno George De Moraes, Marcio Monteiro, José Luis Güntzel
2014 Journal of Integrated Circuits and Systems  
The architectures were synthesized for 90nm, 65nm and 45nm standard cell libraries assuming both nominal and Low-Vdd/High-Vt (LH) cases for maximum and for a given target throughput.  ...  The impacts of both subsampling and LH on delay, power and energy efficiency are analyzed.  ...  ACKNOWLEDGEMENTS This work was partially supported by the Brazilian Federal Agency for the Support and Evaluation of Graduate Education (CAPES) and by the Brazilian Council for Scientific and Technological  ... 
doi:10.29292/jics.v9i1.388 fatcat:jrbittlvwbed5l7xe2z657fv6a
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