You searched on: Author: Marc Salit
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1. The Use of Cause-and-Effect Analysis to Design a High Quality Nano-Cyto-Toxicology Assay
Matthias Rosslein, John T Elliott, Marc L Salit, Elijah J Petersen, Cordula Hirsch, Harald Krug, Peter Wick
An important consideration in developing standards and regulations that govern the production and
use of commercial nanoscale materials is the development of robust and reliable measurements to
assess potential biological effects of these nanomat ...
2. Assessing technical performance in differential gene expression experiments with external spike-
in RNA control ratio mixtures
Sarah A Munro, Steven P Lund, Patrick S Pine, Hans Binder, Djork-Arne Clevert, Ana Conesa, Joaquin Dopazo, Mario Fasold, Sepp Hochreiter, Huixao Hong, Nederah Jafari, David P Kreil, Pawel P Labaj, Yang Liao, Simon Lin, Christopher E Mason, Javier Santoyo, Steven J Schrodi, Leming Shi, Wei Shi, Gordon K Smyth, Nancy Stralis-Pavese, Zhenqiang Su, Charles Wang, Jian Wang, Joshua Xu, Zhan Ye, Yong Yang, Ying Yu, Paul Zumbo, Marc L Salit
There is a critical need for standard approaches to assess, report and compare the technical
performance of genome-scale differential gene expression experiments. Here we assess technical
performance with a proposed standard ,dashboard‰ of metric ...
3. Ontology Analysis if Global Gene Expression Differences of Human Bone Marrow Stromal Cells Cultured on 3D Scaffolds or 2D Films
Bryan A. Baker, Patrick S Pine, Kaushik Chatterjee, Girish Kumar, Jennifer H McDaniel, Marc L Salit, Carl George Simon Jr.
Differences in gene expression of human bone marrow stromal cells (hBMSCs) during culture in three-dimensional (3D) nanofiber scaffolds or on two-dimensional (2D) films were investigated via pathway analysis of microarray mRNA expression profiles. P ...
4. Evaluation of the effect of donor variability on stem cell response to biomaterials
Stephen J Florczyk, Bryan A. Baker, Sumona Sarkar, Jennifer H McDaniel, Patrick S Pine, Marc L Salit, Carl George Simon Jr.
Previous research from our group indicated that nanofiber scaffolds promoted osteogenic
differentiation of human bone marrow stromal cells (hBMSC) and similar gene expression to osteogenic
supplement (OS) induced osteogenic differentiation . ...
5. Why human genome sequencing platforms differ: Integrating sequencing datasets to understand biases and form consensus variant calls
Justin M Zook, Brad Chapman, Winston Hide, Marc L Salit
Hundreds of thousands of differences exist between human whole genome variant calls from different sequencing platforms and variant calling pipelines, but the reasons for these differences are poorly understood. Well-characterized whole genome Refer ...
6. 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- ...
7. 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 ...
8. 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 ...
9. 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 ...
10. 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 ...