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This conclusion is further supported by in vitro microarray data that shows no significant intra-ovary regulation occurring (Additional File 1).
Using this classification, we found remarkable consistency between the experimental in vitro microarray data and Q-PCR results obtained from subjects from real environmental exposure.
Differential gene expression analysis between rank-normalized imputed in vivo and in vitro microarray data revealed a shared set of 39 genes that were among the top 100 overexpressed genes in all three of the analyzed patients (Table 1).
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Combining MIL and structural properties of DNA, it models and predicts in vitro transcription factor bindings more accurately than the widely used k-mer counting methods on in vitro protein binding microarray data for twenty mouse transcription factors.
Details for the in vivo Tn5 mutagenesis procedure, mutant library construction and competitive outgrowth, T7 in vitro transcription/labeling, and microarray data analysis will be provided.
Having used multiple strategies and integrated the PM data with the in vitro and in vivo microarray data, we propose the following hypotheses about streptococcal niche adaptation and switch to hypervirulence: (1) Exposure to the in vivo environment perturbs a substantial number of GAS genes and regulatory networks.
Motivated by the clinical importance of melphalan therapy, we have combined in vitro drug screens and microarray data of B-cell cancer cell lines and identified a melphalan resistance index comprised of 19 genes which may be related to tumor biology.
Our approach thus ensures comparability to previously published in vitro data (including previous microarray data, for example [ 26, 36- 38]).
The "in vitro transcribed" or "IVT" microarray data sets used in this paper are described in a previous publication.
The workflow consists of in vitro drug screens and microarray data of drug naïve carefully selected cancer cell lines combined with regularised multivariate regression.
Twelve genes differentially expressed during in vitro mineralization as for microarray data (6 up- and 6 down-regulated genes) were selected for validation by quantitative real-time PCR (qPCR) according to the following criteria: two genes with FC > 10, two genes with 10 > FC > 2, and two genes with 2 > FC > 1.5 for each cell line.
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