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Multiplex mRNA assay using electrophoretic tags for high-throughput gene expression analysis

Huan Tian, Liching Cao, Yuping Tan, Stephen Williams, Lili Chen, Tracy Matray, Ahmed Chenna, Sean Moore, Vincent Hernandez, Vivian Xiao, Mengxiang Tang and Sharat Singh.

in Nucleic Acids Research

September 2004; p ublished online September 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 6560 words.

We describe a novel multiplexing technology using a library of small fluorescent molecules, termed eTag molecules, to code and quantify mRNA targets. eTag molecules, which have the same...

Attomole quantification and global profile of RNA modifications: Epitranscriptome of human neural stem cells

Maria Basanta-Sanchez, Sally Temple, Suraiya A. Ansari, Anna D'Amico and Paul F. Agris.

in Nucleic Acids Research

February 2016; p ublished online October 2015 .

Journal Article. Subjects: Research Methods in Life Sciences. 7107 words.

Exploration of the epitranscriptome requires the development of highly sensitive and accurate technologies in order to elucidate the contributions of the more than 100 RNA modifications to...

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Microarray-based DNA methylation profiling: technology and applications

Axel Schumacher, Philipp Kapranov, Zachary Kaminsky, James Flanagan, Abbas Assadzadeh, Patrick Yau, Carl Virtanen, Neil Winegarden, Jill Cheng, Thomas Gingeras and Arturas Petronis.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Research Methods in Life Sciences. 9857 words.

This work is dedicated to the development of a technology for unbiased, high-throughput DNA methylation profiling of large genomic regions. In this method, unmethylated and methylated DNA...

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Dual FRET molecular beacons for mRNA detection in living cells

Philip J. Santangelo, Brent Nix, Andrew Tsourkas and Gang Bao.

in Nucleic Acids Research

March 2004; p ublished online March 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 6934 words.

The ability to visualize in real‐time the expression level and localization of specific endogenous RNAs in living cells can offer tremendous opportunities for biological and disease...

Peptide‐linked molecular beacons for efficient delivery and rapid mRNA detection in living cells

Nitin Nitin, Philip J. Santangelo, Gloria Kim, Shuming Nie and Gang Bao.

in Nucleic Acids Research

March 2004; p ublished online March 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 5508 words.

Real‐time visualization of specific endogenous mRNA expression in vivo has the potential to revolutionize medical diagnosis, drug discovery, developmental and molecular biology. However,...

Whole-genome expression profiling through fragment display and combinatorial gene identification

Ats Metsis, Ulf Andersson, Göran Baurén, Patrik Ernfors, Peter Lönnerberg, Andreas Montelius, Mats Oldin, Arno Pihlak and Sten Linnarsson.

in Nucleic Acids Research

September 2004; p ublished online September 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 5184 words.

There is a growing demand for highly parallel gene expression analysis with whole genome coverage, high sensitivity and high accuracy. Open systems such as differential display are capable...

A novel magnetic resonance-based method to measure gene expression in living cells

Sewon Ki, Fuminori Sugihara, Koji Kasahara, Hidehito Tochio, Azusa Okada-Marubayashi, Setsuko Tomita, Masahito Morita, Mitsunori Ikeguchi, Masahiro Shirakawa and Tetsuro Kokubo.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Research Methods in Life Sciences. 4296 words.

In unicellular and multicellular eukaryotes, elaborate gene regulatory mechanisms facilitate a broad range of biological processes from cell division to morphological differentiation. In...

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Monitoring denaturation behaviour and comparative stability of DNA triple helices using oligonucleotide–gold nanoparticle conjugates

Deirdre Murphy, Ramon Eritja and Gareth Redmond.

in Nucleic Acids Research

April 2004; p ublished online April 2004 .

Journal Article. Subjects: Research Methods in Life Sciences. 5210 words.

Gold nanoparticle labels, combined with UV‐visible optical absorption spectroscopic methods, are employed to probe the temperature‐dependent solution properties of DNA triple helices. By...

Establishing an Appropriate Period of Acclimatization Following Transportation of Laboratory Animals

Jennifer A. Obernier and Ransom L. Baldwin.

in ILAR Journal

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Research Methods in Life Sciences. 3696 words.

Stress associated with transportation has widespread effects on physiological systems in laboratory animals, including changes in the cardiovascular, endocrine, immune, central nervous, and...

Assessing Spatial Learning and Memory in Rodents

Charles V. Vorhees and Michael T. Williams.

in ILAR Journal

January 2014; p ublished online January 2014 .

Journal Article. Subjects: Research Methods in Life Sciences. 19914 words.

Maneuvering safely through the environment is central to survival of almost all species. The ability to do this depends on learning and remembering locations. This capacity is encoded in...

Methylation-Specific MLPA (MS-MLPA): simultaneous detection of CpG methylation and copy number changes of up to 40 sequences

Anders O. H. Nygren, Najim Ameziane, Helena M. B. Duarte, Raymon N. C. P. Vijzelaar, Quinten Waisfisz, Corine J. Hess, Jan P. Schouten and Abdellatif Errami.

in Nucleic Acids Research

August 2005; p ublished online August 2005 .

Journal Article. Subjects: Research Methods in Life Sciences. 6264 words.

Copy number changes and CpG methylation of various genes are hallmarks of tumor development but are not yet widely used in diagnostic settings. The recently developed multiplex...

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Absolute quantitative measurement of transcriptional kinetic parameters in vivo

Sukanya Iyer, Bo Ryoung Park and Minsu Kim.

in Nucleic Acids Research

October 2016; p ublished online July 2016 .

Journal Article. Subjects: Research Methods in Life Sciences. 6534 words.

mRNA expression involves transcription initiation, elongation and degradation. In cells, these dynamic processes are highly regulated. However, experimental characterization of the dynamic...

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Immobilized stem–loop structured probes as conformational switches for enzymatic detection of microbial 16S rRNA

Benjamin Bockisch, Thomas Grunwald, Edzard Spillner and Reinhard Bredehorst.

in Nucleic Acids Research

June 2005; p ublished online June 2005 .

Journal Article. Subjects: Research Methods in Life Sciences. 4404 words.

We have designed and evaluated novel DNA stem–loop structured probes for enzymatic detection of nucleic acid targets. These probes constitute a novel class of conformational switches for...

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MSRE-PCR for analysis of gene-specific DNA methylation

Anatoliy A. Melnikov, Ronald B. Gartenhaus, Anait S. Levenson, Natalia A. Motchoulskaia and Victor V. Levenson (Chernokhvostov).

in Nucleic Acids Research

June 2005; p ublished online June 2005 .

Journal Article. Subjects: Research Methods in Life Sciences. 6072 words.

Abnormal DNA methylation is observed in certain promoters of neoplastic cells, although the likelihood of methylation for each individual promoter varies. Simultaneous analysis of many...

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Where does transcription start? 5′-RACE adapted to next-generation sequencing

Fleur A.D. Leenen, Sara Vernocchi, Oliver E. Hunewald, Stephanie Schmitz, Anne M. Molitor, Claude P. Muller and Jonathan D. Turner.

in Nucleic Acids Research

April 2016; p ublished online November 2015 .

Journal Article. Subjects: Research Methods in Life Sciences. 11081 words.

The variability and complexity of the transcription initiation process was examined by adapting RNA ligase-mediated rapid amplification of 5′ cDNA ends (5′-RACE) to Next-Generation...

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cnvCapSeq: detecting copy number variation in long-range targeted resequencing data

Evangelos Bellos, Vikrant Kumar, Clarabelle Lin, Jordi Maggi, Zai Yang Phua, Ching-Yu Cheng, Chui Ming Gemmy Cheung, Martin L. Hibberd, Tien Yin Wong, Lachlan J. M. Coin and Sonia Davila.

in Nucleic Acids Research

November 2014; p ublished online September 2014 .

Journal Article. Subjects: Research Methods in Life Sciences. 6679 words.

Targeted resequencing technologies have allowed for efficient and cost-effective detection of genomic variants in specific regions of interest. Although capture sequencing has been...

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Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes

Sourav Mishra, Hiya Lahiri, Siddhartha Banerjee and Rupa Mukhopadhyay.

in Nucleic Acids Research

May 2016; p ublished online March 2016 .

Journal Article. Subjects: Research Methods in Life Sciences. 7643 words.

So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it...

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Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3′-terminal segment of guide RNA

Vladimir Mekler, Leonid Minakhin, Ekaterina Semenova, Konstantin Kuznedelov and Konstantin Severinov.

in Nucleic Acids Research

April 2016; p ublished online March 2016 .

Journal Article. Subjects: Research Methods in Life Sciences. 5606 words.

CRISPR-Cas9 is widely applied for genome engineering in various organisms. The assembly of single guide RNA (sgRNA) with the Cas9 protein may limit the Cas9/sgRNA effector complex function....

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A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies

Fernando Puente-Sánchez, Jacobo Aguirre and Víctor Parro.

in Nucleic Acids Research

February 2016; p ublished online November 2015 .

Journal Article. Subjects: Research Methods in Life Sciences. 7513 words.

Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads,...

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Probing the elastic limit of DNA bending

Tung T. Le and Harold D. Kim.

in Nucleic Acids Research

September 2014; p ublished online August 2014 .

Journal Article. Subjects: Research Methods in Life Sciences. 7741 words.

Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured...

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