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Author: Marc Salit
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1. Characterization of In Vitro Transcription Amplification Linearity and Variability in the Low Copy Number Regime using ERCC Spike Ins
Jason G Kralj, Marc L Salit
Characterization of whole transcriptomes from small RNA samples (less than 1 ng total RNA) has been a major challenge. Typically, samples are extracted and purified, amplified by in vitro transcription (IVT), and then subjected to genome- ...
2. Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing
Justin M Zook, Daniel Victor Samarov, Jennifer H McDaniel, Shurjo Sen, Marc L Salit
While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing
errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can ...
3. Morphological Changes Driven by Nanofibrous Scaffolds Induce Marrow Stromal Cell Osteogenesis
Carl George Simon Jr, Kaushik Chatterjee, Christopher K. Tison, Girish Kumar, Patrick S Pine, Marc L Salit, Jennifer H McDaniel, Marian F Young
Cells are sensitive to tissue scaffold architecture and these cell-material interactions drive cell functions critical in tissue regeneration. Results presented here demonstrate that nanofiber scaffolds force primary human bone marrow stromal cells ...
4. Synthetic spike-in standards for RNA-seq experiments
Marc L Salit, Lichun Jiang, Felix Schlesinger,, Brian Oliver, Carrie Davis, Yu Zhang, Renhua Li, Thomas R Gingeras
High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of different protocols and platforms remain. We used a newly developed pool of 96 synthetic RNAs w ...
5. Contributions of the EMERALD project to assessing and improving microarray data quality
Vidar Beisvag, Audrey Kauffmann, James Malone, Carole Foy, Marc L Salit, Schimmel Heinz, Erik Bongcam-Rudloff, Ulf Landegren, Helen Parkinson, Wolfgang Huber, Alvis Brazma, Arne K Sandvik, Martin Kuiper
While MIAME standards have helped to increase the value of microarray data deposited in public databases like ArrayExpress and GEO, limited means have been available to assess the quality of the data or to identify the procedures that were used to no ...
6. Exploring the use of internal and external controls for assessing microarray technical performance
Katrice A Lippa, David Lee Duewer, Marc L Salit, Laurence Game, Helen Causton
Background: The maturing of gene expression microarray science and interest in the use of microarray-based applications for clinical and diagnostic applications calls for objective measures of quality. This manuscript presents a retrospective study c ...
7. Image-Based Feedback Control for Real-Time Sorting of Microspheres in a Microfluidic Device
Matthew S Munson, James Spotts, Antti Niemisto, Jyrki Selinummi, Jason G Kralj, Marc L Salit, Adrian Ozinsky
We have developed a fully automated control system to distribute user-defined numbers of antibody-functionalized fluorescent beads (scalable from tens to hundreds) to addressable assay chambers within a microfluidic PDMS device. We report an automat ...
8. Use of Standard Reference Material 2242 (Relative Intensity Correction Standard for Raman Spectroscopy) for Microarray Scanner
Mary B Satterfield, Marc L Salit, Steven J Choquette
As a critical component of any microarray experiment, scanner performance has the potential to contribute variability and bias,
the magnitude of which is usually not quantified. Using Standard Reference Material (SRM) 2242, certified for Raman spec ...
9. High-accuracy epitaxial A1GaAs composition determination with inductivity coupled plasma optical emission spectroscopy
Kristine A Bertness, C M Wang, Marc L Salit, Gregory C Turk, Therese A. Butler, Albert J. Paul, Lawrence H Robins
10. Standards in Gene Expression Microarray Experiments
Marc L Salit
The use of standards in gene expression measurements with DNA microarrays is ubiquitous—they just are not yet the kind of standards that have yielded microarray gene expression profiles that can be readily compared across different studies and differ ...