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The Power Decoder simulator for the evaluation of pooled shRNA screen performance
Jesse Stombaugh, Abel Licon, Žaklina Strezoska, Joshua Stahl, Sarah Bael Anderson, Michael Banos, Anja van Brabant Smith, Amanda Birmingham, Annaleen Vermeulen

Power Decoder (written in R and Python) simulates shRNA pooled screening experiments in silico to allow for the estimation of a screen’s statistical power. Populations of shRNAs were engineered in such a way that the magnitude of depletion and enrichment was known, then using the negative binomial distribution, an in silico model was developed to successfully resemble data from an actual laboratory experiment.

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Knockdown of long noncoding RNAs in breast cancer
1 Jennii Luu, 2 Jesper Maag, 1 Yanny Handoko, 3 Richard Redvers, 3,4 Robin L. Anderson, 5 Maren M. Gross , 2 Marcel E. Dinger, and 1,3 Kaylene J. Simpson 1 Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre; 2 Genome Informatics, The Kinghorn Cancer Centre, The Garvan Institute of Medical Research; 3 Metastasis Research Laboratory, Peter MacCallum Cancer Centre, 4 Sir Peter MacCallum Department of Oncology, University of Melbourne;

RNAi global collaboration study using Lincode siRNA in a primary screen of tumor and nontumor breast cell lines. Hundreds of lncRNAs are found to affect viability and cell morphology of breast cancer. Presented at Keystone Symposia on Long Noncoding RNAs: From Evolution to Function, Mar 15 - Mar 20, 2015.

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Specificity of highly potent miRNA inhibitors
Barbara Robertson, Andrew Dalby, Yuriy Fedorov, Jon Karpilow, Anastasia Khvorova1, Devin Leake, Annaleen Vermeulen

miRNA inhibitors are invaluable tools for elucidating the roles of miRNAs. However, potent inhibitors may also affect other miRNAs. To understand the potential cross-reactivity of miRNA inhibitors, various miRNA inhibitor designs were systematically tested. We demonstrate that mismatches both within and outside the seed region of the miRNA interfere with inhibition. Our findings indicate that features important for natural miRNA target recognition are also important for inhibitor specificity.

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Alternative miRNA design for therapeutic RNAi applications
Anja van Brabant Smith, Barb Robertson, Annaleen Vermeulen, Christina Yamada, Angela Reynolds, Anastasia Khvorova, Devin Leake

For in vivo applications, the design of miRNA inhibitors and miRNA mimics must be optimized for stability and potency. However, stabilized miRNA mimic molecules can lose functionality compared to standard miRNA mimic molecules due, in part, to the activity of the stabilized passenger strand acting as a miRNA inhibitor. We discuss how mismatches affect the activity of the stabilized miRNA mimics, perhaps by generating a passenger strand that is less functional as an inhibitor molecule.

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Cas9 driven by an optimal promoter improves gene editing in eukaryotic cell lines when paired with synthetic crRNA and tracrRNA
Amanda Haupt, Emily Anderson, Žaklina Strezoska, Hidevaldo Machado, Shawn McClelland, Maren Mayer, Adam Rocker, Annaleen Vermeulen, Amanda Birmingham, Melissa Kelley, Anja Smith

Presented here are results on the efficiency of using synthetic crRNA and tracrRNA to introduce gene editing events when co-transfected with a plasmid expressing Cas9. We explored the use of antibiotic and fluorescence activated cell sorting (FACS) methods for enrichment of cells that have undergone gene editing, and the use of multiple promoters to increase efficiency of gene editing with Cas9 and synthetic tracrRNA and crRNAs.

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Specificity and functionality of microRNA inhibitors
Barbara Robertson, Andrew Dalby, Jon Karpilow, Anastasia Khvorova, Devin Leake and Annaleen Vermeulen

Our findings indicate that features important for natural miRNA target recognition also appear to be important for inhibitor specificity. Understanding the specificity of inhibitors allows for better interpretation of inhibitor activity in endogenous systems.

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Identification of microRNA targets using microRNA modulation techniques and gene expression arrays
Emily M. Anderson, Maren Mayer, Kevin Sullivan, Barbara Robertson, Žaklina Strezoska, Annaleen Vermeulen, and Devin Leake

By examining the overlap of messages down-regulated by miRNA mimics and up-regulated by miRNA inhibitors, we robustly identify miRNA-regulated messages, many of which have canonical seed matches and some which are not identied by standard target prediction programs.

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siRNA Screening: Development of Hit Stratification Strategies
Žaklina Strezoska, Annaleen Vermeulen, Emily M. Anderson, Anja Smith, Devin Leake

This poster compares different approaches to hit stratification and validation after an initial screen. Standard siRNA reagents deconvoluted from a pooled set of four were compared to a pooled set of four specificity enhanced reagents. High confidence hits were similar. To explore the validity of low confidence hits, a chimeric approach was used whereby a gene-specific seed sequence was introduced into a non-targeting siRNA scaffold. This work resulted in new hit stratification strategies.

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The Chemical Synthesis of Long and Highly Modified RNA using 2'-ACE Chemistry
Xiaoqin Cheng, Kristina Larson, Letitia Kwok, David Mierzejewski, Shawn Begay, Randy Rauen, Kelly Grimsley, Kaizhang He, Michael Delaney, David Kitchen, Amanda Haas, Melissa Kelley, Anja van Brabant Smith

Dharmacon has previously developed a novel RNA synthesis chemistry making RNA synthesis as reliable, accessible and of comparable quality as routinely observed in DNA synthesis.

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Peanut Allergy: An epidemiologic analysis of a large database
Leickly, FE, Vitapur, G, and Kloepfer, K

Over three years, 700 children with a peanut story - either peanut sensitization or peanut allergy- were asked to participate in a database.

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Scientific News
Exploring Living cells
JPK reports the exploration of living cells using nanoscale and single molecule techniques through the application of scanning probe microscopy.
The Perfect Partnership: Research & Industry; Software & Instrumentation. It really starts to come together at ASMS 2015
Collaboration and knowledge-sharing were evident everywhere: on the bus, in the hallways and in the bars. This article aims to capture this theme and share with you some of the fruits of this coming together of science and industry.
Designing New Pain Relief Drugs
Researchers have identified the molecular interactions that allow capsaicin to activate the body’s primary receptor for sensing heat and pain, paving the way for the design of more selective and effective drugs to relieve pain.
Antibody Pries Loose Bacteria’s Grip
Study finds novel method of improving antibody efficacy.
CLAIRE Brings Electron Microscopy to Soft Materials
CLAIRE works by essentially combining the best attributes of optical and scanning electron microscopy into a single imaging platform.
Sample & Analysis Tracking in Oncogenomic Experiments
The study outlines Onco-STS, a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments.
Pittcon Announces Wide Variety of Short Courses
Courses range from beginner and intermediate to advanced levels.
Ultra-enriched Silicon Paves the Road to Quantum Computing
Using a relatively straightforward technique, a team of NIST researchers has created what may be the most highly enriched silicon currently being produced.
BioClinica and Rutgers University Announce Research Project Results
Scientific Partnership Aims to Expand Automation of Clinical Trial Image Data Analysis
Leading Japanese CRO Standardizes on Thermo Scientific Watson LIMS
JCL Bioassay uses Thermo Scientific Watson LIMS to optimize communication, data management and quality control during U.S. expansion.
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