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CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity

Blake Carrington, Gaurav K. Varshney, Shawn M. Burgess and Raman Sood.

in Nucleic Acids Research

December 2015; p ublished online August 2015 .

Journal Article. Subjects: Research Methods in Life Sciences. 4955 words.

CRISPR/Cas9 has emerged as a versatile genome-engineering tool that relies on a single guide RNA (sgRNA) and the Cas9 enzyme for genome editing. Simple, fast and economical methods to...

Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization

Mauro D. Locati, Inez Terpstra, Wim C. de Leeuw, Mateusz Kuzak, Han Rauwerda, Wim A. Ensink, Selina van Leeuwen, Ulrike Nehrdich, Herman P. Spaink, Martijs J. Jonker, Timo M. Breit and Rob J. Dekker.

in Nucleic Acids Research

August 2015; p ublished online April 2015 .

Journal Article. Subjects: Research Methods in Life Sciences. 6168 words.

There is an increasing interest in complementing RNA-seq experiments with small-RNA (sRNA) expression data to obtain a comprehensive view of a transcriptome. Currently, two main...

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Characterization of zebrafish Rad52 and replication protein A for oligonucleotide-mediated mutagenesis

Nobuhiro Takahashi and Igor B. Dawid.

in Nucleic Acids Research

August 2005; p ublished online August 2005 .

Journal Article. Subjects: Research Methods in Life Sciences. 5809 words.

Zebrafish has become a favorite model organism not only in genetics and developmental biology, but also for the study of cancer, neuroscience and metabolism. However, strategies for reverse...

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Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays

Paul M. K. Gordon and Christoph W. Sensen.

in Nucleic Acids Research

September 2004; p ublished online September 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 6336 words.

We have developed a software package called Osprey for the calculation of optimal oligonucleotides for DNA sequencing and the creation of microarrays based on either PCR-products or...

Multiplexed miRNA northern blots via hybridization chain reaction

Maayan Schwarzkopf and Niles A. Pierce.

in Nucleic Acids Research

September 2016; p ublished online June 2016 .

Journal Article. Subjects: Research Methods in Life Sciences. 3910 words.

Northern blots enable detection of a target RNA of interest in a biological sample using standard benchtop equipment. miRNAs are the most challenging targets as they must be detected with a...

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A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor

Ramesh K. Jha, Theresa L. Kern, Youngchang Kim, Christine Tesar, Robert Jedrzejczak, Andrzej Joachimiak and Charlie E. M. Strauss.

in Nucleic Acids Research

September 2016; p ublished online August 2016 .

Journal Article. Subjects: Research Methods in Life Sciences. 8321 words.

A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires...

Efficient CRISPR-rAAV engineering of endogenous genes to study protein function by allele-specific RNAi

Manuel Kaulich, Yeon J. Lee, Peter Lönn, Aaron D. Springer, Bryan R. Meade and Steven F. Dowdy.

in Nucleic Acids Research

April 2015; p ublished online January 2015 .

Journal Article. Subjects: Research Methods in Life Sciences. 4052 words.

Gene knockout strategies, RNAi and rescue experiments are all employed to study mammalian gene function. However, the disadvantages of these approaches include: loss of function adaptation,...

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mazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis

Xiao-Zhou Zhang, Xin Yan, Zhong-Li Cui, Qing Hong and Shun-Peng Li.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Research Methods in Life Sciences. 4753 words.

Here, we present a novel method for the directed genetic manipulation of the Bacillus subtilis chromosome free of any selection marker. Our new approach employed the Escherichia coli toxin...

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An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes

Kévin Le Brigand, Roslin Russell, Chimène Moreilhon, Jean-Marie Rouillard, Bernard Jost, Franck Amiot, Virginie Magnone, Christine Bole-Feysot, Philippe Rostagno, Virginie Virolle, Virginie Defamie, Philippe Dessen, Gary Williams, Paul Lyons, Géraldine Rios, Bernard Mari, Erdogan Gulari, Philippe Kastner, Xavier Gidrol, Tom C. Freeman and Pascal Barbry.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Research Methods in Life Sciences. 9647 words.

Two collections of oligonucleotides have been designed for preparing pangenomic human and mouse microarrays. A total of 148 993 and 121 703 oligonucleotides were designed against human and...

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Large‐scale determination of the methylation status of retrotransposons in different tissues using a methylation tags approach

Konstantin Khodosevich, Yuri Lebedev and Eugene D. Sverdlov.

in Nucleic Acids Research

February 2004; p ublished online February 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 5019 words.

A technique for simultaneous determination of the methylation status of numerous loci containing retroelements (REs) is reported. It is based on the observation that methylated and...

A high‐throughput method to monitor the expression of microRNA precursors

Thomas D. Schmittgen, Jinmai Jiang, Qian Liu and Liuqing Yang.

in Nucleic Acids Research

March 2004; p ublished online March 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 6687 words.

microRNAs (miRNAs) are small, functional, non‐coding RNAs. miRNAs are transcribed as long primary transcripts (primary precursors) that are processed to the ∼75 nt precursors (pre‐miRNAs)...

Oligonucleotide hybridization studied by a surface plasmon diffraction sensor (SPDS)

Fang Yu, Danfeng Yao and Wolfgang Knoll.

in Nucleic Acids Research

May 2004; p ublished online May 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 4811 words.

A novel label‐free biosensor concept based on surface plasmon‐enhanced diffraction by micro‐ patterned interfaces was applied to the study of hybridization reactions of target DNA...

DNA analysis with multiplex microarray-enhanced PCR

A. Pemov, H. Modi, D. P. Chandler and S. Bavykin.

in Nucleic Acids Research

January 2005; p ublished online January 2005 .

Journal Article. Subjects: Research Methods in Life Sciences. 6725 words.

We have developed a highly sensitive method for DNA analysis on 3D gel element microarrays, a technique we call multiplex microarray-enhanced PCR (MME-PCR). Two amplification strategies are...

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Diagnostic application of padlock probes—multiplex detection of plant pathogens using universal microarrays

Marianna Szemes, Peter Bonants, Marjanne de Weerdt, Johan Baner, Ulf Landegren and Cor D. Schoen.

in Nucleic Acids Research

January 2005; p ublished online January 2005 .

Journal Article. Subjects: Research Methods in Life Sciences. 7521 words.

Padlock probes (PLPs) are long oligonucleotides, whose ends are complementary to adjacent target sequences. Upon hybridization to the target, the two ends are brought into contact, allowing...

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MicroRNA expression profiling of single whole embryonic stem cells

Fuchou Tang, Petra Hajkova, Sheila C. Barton, Kaiqin Lao and M. Azim Surani.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Research Methods in Life Sciences. 3603 words.

MicroRNAs (miRNAs) are a class of 17–25 nt non-coding RNAs that have been shown to have critical functions in a wide variety of biological processes during development. Recently developed...

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Review of Elephant Endotheliotropic Herpesviruses and Acute Hemorrhagic Disease

Simon Y. Long, Erin M. Latimer and Gary S. Hayward.

in ILAR Journal

February 2016; p ublished online February 2016 .

Journal Article. Subjects: Research Methods in Life Sciences. 11742 words.

More than 100 young captive and wild Asian elephants are known to have died from a rapid-onset, acute hemorrhagic disease caused primarily by multiple distinct strains of two closely...

Down-regulation of MDM2 and activation of p53 in human cancer cells by antisense 9-aminoacridine–PNA (peptide nucleic acid) conjugates

Takehiko Shiraishi and Peter E. Nielsen.

in Nucleic Acids Research

September 2004; p ublished online September 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 6101 words.

A series of peptide nucleic acid (PNA) oligomers targeting the mdm2 oncogene mRNA has been tested for the ability to inhibit the growth of JAR cells. The effect of these PNAs on the cells...

Systematic analysis of bicistronic reporter assay data

Jonathan L. Jacobs and Jonathan D. Dinman.

in Nucleic Acids Research

November 2004; p ublished online November 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 7220 words.

Bicistronic reporter assay systems have become a mainstay of molecular biology. While the assays themselves encompass a broad range of diverse and unrelated experimental protocols, the...

A Systems Biology Approach Utilizing a Mouse Diversity Panel Identifies Genetic Differences Influencing Isoniazid-Induced Microvesicular Steatosis

Rachel J. Church, Hong Wu, Merrie Mosedale, Susan J. Sumner, Wimal Pathmasiri, Catherine L. Kurtz, Mathew T. Pletcher, John S. Eaddy, Karamjeet Pandher, Monica Singer, Ameesha Batheja, Paul B. Watkins, Karissa Adkins and Alison H. Harrill.

in Toxicological Sciences

August 2014; p ublished online August 2014 .

Journal Article. Subjects: Medical Toxicology; Research Methods in Life Sciences. 7547 words.

Isoniazid (INH), the mainstay therapeutic for tuberculosis infection, has been associated with rare but serious hepatotoxicity in the clinic. However, the mechanisms underlying...

Simple and highly efficient BAC recombineering using galK selection

Søren Warming, Nina Costantino, Donald L. Court, Nancy A. Jenkins and Neal G. Copeland.

in Nucleic Acids Research

February 2005; p ublished online February 2005 .

Journal Article. Subjects: Research Methods in Life Sciences; Molecular and Cell Biology. 8230 words.

Recombineering allows DNA cloned in Escherichia coli to be modified via lambda (λ) Red-mediated homologous recombination, obviating the need for restriction enzymes and DNA ligases to modify...

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