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Efficient digest of high-throughput sequencing data in a reproducible report

Zhe Zhang, Jeremy Leipzig, Ariella Sasson, Angela M Yu, Juan C Perin, Hongbo M Xie, Mahdi Sarmady, Patrick V Warren, Peter S White
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results: We developed bamchop, a robust program to efficiently summarize key statistical metrics of HTS data stored in BAM files, and to visually present the results in a formatted report.  ...  High-throughput sequencing (HTS) technologies are spearheading the accelerated development of biomedical research.  ...  This article has been published as part of BMC Bioinformatics Volume 14 Supplement 11, 2013: Selected articles from The Second Workshop on Data Mining of Next-Generation Sequencing in conjunction with  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s11-s3">doi:10.1186/1471-2105-14-s11-s3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24564231">pmid:24564231</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3846741/">pmcid:PMC3846741</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/glvvga2zxjeotkdd4mvso26yde">fatcat:glvvga2zxjeotkdd4mvso26yde</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3846741/PMC3846741-1471-2105-14-S11-S3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b0/5b/b05b5493fb31d125124f85dfc6f3c53aa73d54db.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-s11-s3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846741" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SeqRepo: A system for managing local collections of biological sequences

Reece K. Hart, Andreas Prlić, Ruslan Kalendar
<span title="2020-12-03">2020</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
However, for high-throughput and clinical applications, local sequence collections are essential for performance, stability, privacy, and reproducibility.  ...  Results Here we describe SeqRepo, a novel system for building a local, high-performance, non-redundant collection of biological sequences.  ...  As can be expected, there is a significant difference in overall throughput between the different approaches of accessing sequence data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0239883">doi:10.1371/journal.pone.0239883</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33270643">pmid:33270643</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nll22vjngfb2dklabpoj2jkdwq">fatcat:nll22vjngfb2dklabpoj2jkdwq</a> </span>
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DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines

Alper Kucukural, Manuel Garber, Onur Yukselen, Osman Turkyilmaz, Ahmet Ozturk, Isabelle Girard, Roy Martin
<span title="">2020</span> <i title="Association of Biomolecular Resource Facilities"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zlb4hq4hkfgptl2zq3dbo5nqpa" style="color: black;">Journal of Biomolecular Techniques</a> </i> &nbsp;
The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) are transforming biological research.  ...  The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline.  ...  Background The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) are transforming biological research.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32831734">pmid:32831734</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7424693/">pmcid:PMC7424693</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ut4ycgglvfht3kzpz54skkefre">fatcat:ut4ycgglvfht3kzpz54skkefre</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200829134931/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7424693&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7424693" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A native chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in strawberry fruits

Xiaorong Huang, Qinwei Pan, Ying Lin, Tingting Gu, Yi Li
<span title="2020-02-03">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7g2xzafrze7jhzts3tizvsi7e" style="color: black;">Plant Methods</a> </i> &nbsp;
The efficiency and reproducibility of our optimized N-ChIP protocol are validated by both qRT-PCR and high-throughput sequencing.  ...  However, a validated ChIP method has not been reported in strawberry, probably due to its high levels of polysaccharides which affect the quality of prepared chromatin and the efficiency of immunoprecipitation  ...  Han Chen (Nanjing Agricultural University) for their suggestions for ChIP experiments and data processing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13007-020-0556-z">doi:10.1186/s13007-020-0556-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32025237">pmid:32025237</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6998251/">pmcid:PMC6998251</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nfb2kdr3a5cfzmaedjp4ve7ejq">fatcat:nfb2kdr3a5cfzmaedjp4ve7ejq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200213054330/https://plantmethods.biomedcentral.com/track/pdf/10.1186/s13007-020-0556-z" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/04/74/0474bfaacaf9f1123a0942b3bb9523c755f8d383.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13007-020-0556-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6998251" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Development and application of a high throughput carbohydrate profiling technique for analyzing plant cell wall polysaccharides and carbohydrate active enzymes

Xiaofei Li, Peter Jackson, Denis V Rubtsov, Nuno Faria-Blanc, Jenny C Mortimer, Simon R Turner, Kristian B Krogh, Katja S Johansen, Paul Dupree
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/znq2tzejsjgh7awy37u4f6erxa" style="color: black;">Biotechnology for Biofuels</a> </i> &nbsp;
High throughput, DASH).  ...  Results: A method and software was developed allowing the use of a DNA sequencer to profile oligosaccharides derived from plant cell wall polysaccharides (DNA sequencer-Assisted Saccharide analysis in  ...  Acknowledgements We thank John Lester and the Biochemistry Dept Sequencing Facility, University of Cambridge for use of the DNA sequencer, and Nadine Anders for comments on the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1754-6834-6-94">doi:10.1186/1754-6834-6-94</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23819705">pmid:23819705</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3717103/">pmcid:PMC3717103</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2osiackpaffthiccvrriavbn3y">fatcat:2osiackpaffthiccvrriavbn3y</a> </span>
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High-Throughput and Accurate Determination of Transgene Copy Number and Zygosity in Transgenic Maize: From DNA Extraction to Data Analysis

Fang Liu, Jinkui Cheng, Xuhua Liu, Xi-Qing Wang
<span title="2021-11-19">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
In this study, the target sequence of the previously reported endogenous reference gene hmg was analyzed using 633 maize inbred lines, and two SNPs were observed.  ...  With the high-throughput DNA extraction and automated data analysis procedures developed in this study, nearly 2700 samples could be analyzed within eight hours by two persons.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms222212487">doi:10.3390/ijms222212487</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34830369">pmid:34830369</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8619409/">pmcid:PMC8619409</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pbuygyaqtndnxkjongxpzmavhq">fatcat:pbuygyaqtndnxkjongxpzmavhq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220430131348/https://mdpi-res.com/d_attachment/ijms/ijms-22-12487/article_deploy/ijms-22-12487.pdf?version=1637318410" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6a/4b/6a4b255bcb4f4c0e9a3a34da3e0c5bc3a7de453e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms222212487"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8619409" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Improving the Biomarker Pipeline

C. H. Borchers, C. E. Parker
<span title="2010-10-12">2010</span> <i title="American Association for Clinical Chemistry (AACC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b3kmrecbc5hnhkzfkc3zkbultm" style="color: black;">Clinical Chemistry</a> </i> &nbsp;
The reproducibility, however, was predicated on the reproducibility of all of the steps in the analysis, from digestion to data analysis.  ...  The authors also used a "standard plasma" sample to correct for day-to-day variations in digestion efficiency.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1373/clinchem.2010.155705">doi:10.1373/clinchem.2010.155705</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20940327">pmid:20940327</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gtd3kicl55gndcawsqd5bg2dl4">fatcat:gtd3kicl55gndcawsqd5bg2dl4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170825153030/http://clinchem.aaccjnls.org/content/clinchem/56/12/1786.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5e/d8/5ed8dfcbfe9f696e049a8471773be8ca10c9e777.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1373/clinchem.2010.155705"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Easier, Better, Faster, Stronger: Improved Methods for RNA-Protein Interaction Studies

Nazmul Haque, J. Robert Hogg
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/afqwz322bfdapd7r446dhqqbbm" style="color: black;">Molecular Cell</a> </i> &nbsp;
RNAs covalently linked to the target RBP are partially digested to generate short sequence tags suitable for cDNA library preparation and high-throughput sequencing.  ...  Methods combining UV-crosslinking and RNA binding protein (RBP) immunoprecipitation with high-throughput sequencing (CLIP-Seq) promise to allow comprehensive highresolution identification of all of the  ...  In contrast, cDNA generated in eCLIP is ligated to a second adapter using optimized ligation methods. The products are then amplified by PCR and analyzed by high-throughput sequencing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.molcel.2016.05.019">doi:10.1016/j.molcel.2016.05.019</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27259196">pmid:27259196</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5592797/">pmcid:PMC5592797</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nvgdtizcw5a5lo53zdmzixdsi4">fatcat:nvgdtizcw5a5lo53zdmzixdsi4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191202140005/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5592797&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/78/e9/78e9ad8bd6173fe9301ecebf20046b87df44559d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.molcel.2016.05.019"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592797" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Quantitative Analysis of Nucleic Acids - the Last Few Years of Progress

Chunming Ding, Charles R. Cantor
<span title="2004-01-31">2004</span> <i title="Korean Society for Biochemistry and Molecular Biology - BMB Reports"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/k2dhmjjc5ffvbbvzs2zzcdrbce" style="color: black;">BMB Reports</a> </i> &nbsp;
The technologies are also evaluated in terms of a few key aspects of nucleic acids quantification such as accuracy, sensitivity, specificity, cost and throughput.  ...  In this review, we first give a brief overview of how DNA and RNA quantifications are carried out.  ...  SAGE also has high throughput due to the high capacity of capillary sequencers. Neither real time PCR nor real competitive PCR has the same level of throughput in terms of gene numbers.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5483/bmbrep.2004.37.1.001">doi:10.5483/bmbrep.2004.37.1.001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14761298">pmid:14761298</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xd6py4ft3jbcpo57mawudcoy6a">fatcat:xd6py4ft3jbcpo57mawudcoy6a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20061020075825/http://ihome.cuhk.edu.hk:80/~b110723/PDFs/Ding-Cantor_JBMB-01-2004.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/9c/f09cc625375979fd251fefa9dc58b99eeb1a3266.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5483/bmbrep.2004.37.1.001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule Sequencer

Masayoshi Itoh, Miki Kojima, Sayaka Nagao-Sato, Eri Saijo, Timo Lassmann, Mutsumi Kanamori-Katayama, Ai Kaiho, Marina Lizio, Hideya Kawaji, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki (+1 others)
<span title="2012-01-30">2012</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Cap analysis of gene expression (CAGE) is a 59 sequence tag technology to globally determine transcriptional starting sites in the genome and their expression levels and has most recently been adapted  ...  Methodology: In this study we set out to adapt the protocol to a robotic workflow, which would increase throughput and reduce handling.  ...  Milos in Helicos BioSciences Corporation for support of sequencing operations. We thank T. Teraoka and K. Murayama in TECAN for the establishment of stage layout and all scripts. We also thank S.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0030809">doi:10.1371/journal.pone.0030809</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22303458">pmid:22303458</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3268765/">pmcid:PMC3268765</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a2hevyytynck5py2ij25jfblqm">fatcat:a2hevyytynck5py2ij25jfblqm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171003013830/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0030809&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4f/c7/4fc7a523500b6bbc7bb8877af0fd91ed254bacae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0030809"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268765" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

HRIBO - High-throughput analysis of bacterial ribosome profiling data [article]

Rick Gelhausen, Florian Heyl, Sarah Lauren Svensson, Kathrin Froschauer, Lydia Hadjeras, Cynthia M. Sharma, Florian Eggenhofer, Rolf Backofen
<span title="2020-04-29">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Results: We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data.  ...  While pipelines are available to analyze Ribo-seq data, none are designed explicitly for the analysis of Ribo-seq data from prokaryotes, nor are they focused on the discovery of unannotated open reading  ...  Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal, 17(1):10-12, 2011. 11. Elvis Ndah et al.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.04.27.046219">doi:10.1101/2020.04.27.046219</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6otidwtfbnbobh77lyczhorsoa">fatcat:6otidwtfbnbobh77lyczhorsoa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711103136/https://www.biorxiv.org/content/biorxiv/early/2020/04/29/2020.04.27.046219.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/99/5b/995bad910d95ee5ca41121a609d3d5f053f9ff5c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.04.27.046219"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system

Fang Yang, Yingying Lei, Meiling Zhou, Qili Yao, Yichao Han, Xiang Wu, Wanshun Zhong, Chenghang Zhu, Weize Xu, Ran Tao, Xi Chen, Da Lin (+9 others)
<span title="2017-11-20">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
While recent state-of-the-art yeast two-hybrid (Y2H) systems improved screening efficiency, either individual colony isolation, library preparation arrays, gene barcoding or massive sequencing are still  ...  The integrated fragments were digested by MmeI and subjected to deep sequencing to decode the interaction matrix.  ...  These digested products were ligated with Illumina P5 and P7 adapters to generate a high-throughput sequencing library ( Figure 3D ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx1173">doi:10.1093/nar/gkx1173</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29165646">pmid:29165646</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5815087/">pmcid:PMC5815087</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fpsjrj2cqra2plknp7tt6l6zli">fatcat:fpsjrj2cqra2plknp7tt6l6zli</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302221859/http://pdfs.semanticscholar.org/bd92/89d0170fdba0c0da8c1cc93de582309a35f6.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/bd/92/bd9289d0170fdba0c0da8c1cc93de582309a35f6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx1173"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5815087" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An IS6110-targeting fluorescent amplified fragment length polymorphism alternative to IS6110 restriction fragment length polymorphism analysis for Mycobacterium tuberculosis DNA fingerprinting

N. Thorne, J.T. Evans, E.G. Smith, P.M. Hawkey, S. Gharbia, C. Arnold
<span title="">2007</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wy5s4xn72rajbp3jnnghxa6lhq" style="color: black;">Clinical Microbiology and Infection</a> </i> &nbsp;
Comparison with an in-silico digestion of strain H37Rv showed that fAFLP-detected fragments were highly specific in vitro. The reproducibility of repeated digestions of strain H37Rv was 100%.  ...  The new method was tested for specificity and reproducibility, and compared with the standard reference IS6110 restriction fragment length polymorphism (RFLP) method for a panel of 78 isolates.  ...  TaqI works efficiently at a high temperature (65°C) and facilitates the dissociation of complementary strands of the GC-rich (i.e., high T m ) genomic DNA to allow more efficient and complete digestion  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1469-0691.2007.01783.x">doi:10.1111/j.1469-0691.2007.01783.x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17803750">pmid:17803750</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vrpjqbf5qfbf7hic7udwi3ilhe">fatcat:vrpjqbf5qfbf7hic7udwi3ilhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222032447/https://core.ac.uk/download/pdf/82245302.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0f/2e/0f2e8d6842364890797b9867dd1fd1628e2cfbcf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1469-0691.2007.01783.x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Automated sample preparation for high-throughput single-cell proteomics [article]

Harrison Specht, Guillaume Harmange, David H Perlman, Edward Emmott, Zachary Niziolek, Bogdan Budnik, Nikolai Slavov
<span title="2018-08-25">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The results demonstrate low noise and high technical reproducibility.  ...  We integrated mPOP lysis with the Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) sample preparation, and benchmarked the quantification of such samples on a Q-exactive instrument.  ...  Acknowledgments: We thank A. Petelski, R. G. Huffman, A. Chen, and J. Neveu, for assistance,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/399774">doi:10.1101/399774</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zf6zhqte4vbh5gi3opl2l5dbx4">fatcat:zf6zhqte4vbh5gi3opl2l5dbx4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502064336/https://www.biorxiv.org/content/biorxiv/early/2018/08/25/399774.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/33/43/3343f1ea3772930f04572b925a4d10fd39528608.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/399774"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Comparison between procedures using SDS for shotgun proteomic analyses of complex samples

Michael S. Bereman, Jarrett D. Egertson, Michael J. MacCoss
<span title="2011-06-08">2011</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fuys75pzlrec5izxlpab5g6jue" style="color: black;">Proteomics</a> </i> &nbsp;
The SDS spin column procedure affords a conservative 4-fold improvement in throughput, is more reproducible, less expensive (i.e., requires less materials), and identifies between 30-107% more peptides  ...  Filter aided sample preparation (FASP) and a new sample preparation method using a modified commercial SDS removal spin column are quantitatively compared in terms of their performance for shotgun proteomic  ...  Acknowledgments The authors greatly acknowledge the financial support from the National Institutes of Health (R01 DK069386, U01 HG004263, and P41 RR011823).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pmic.201100045">doi:10.1002/pmic.201100045</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21656683">pmid:21656683</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3517139/">pmcid:PMC3517139</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p4t27r3y4vcpfbo4wcqs33joxe">fatcat:p4t27r3y4vcpfbo4wcqs33joxe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220225161731/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3517139&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6c/88/6c88d87aacced5defffaa4fa000f960947cbf742.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pmic.201100045"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517139" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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