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However, analysis of the microarray experiment reported here revealed that E. coli infection of mammary gland quarters can have a profound effect on gene expression in other, uninfected quarters.
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In contrast to our results, other whole genome microarray experiments reported that Mediator associates with many genes at both promoter and coding regions in S. cerevisiae [11] and S. pombe [12] cells grown under non-stressed conditions (synthetic complete medium).
In order to establish gene expression profiles for both CAN nucleases we analyzed microarray experiments reported by Genevestigator [ 29].
Raw data for the microarray experiments reported herein are stored in the GenEx database and can be accessed on request [ 77].
Raw and normalized data for the microarray experiments reported herein are stored in the public repositories ArrayExpress (accession no E-MEXP-488) [ 52].
The microarray experiments reported by Wong et al. [ 19] investigating gene expression in plants stressed in growth cabinets is accessible at NCBI's Gene Expression Omnibus (GEO) database [ 59], accession GSE2981.
The raw and processed data from the ChIP-Seq, RNA-Seq and microarray experiments reported in this publication have been submitted to the NCBI Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo) and assigned the identifier GSE48086.
Although the MIAME (minimum information about a microarray experiment) report defines standards for information needed for reporting microarray experiments [ 19], it does not describe or quantify variabilities in the experiments.
Pre-microarray validation was performed from the same samples used for the microarray experiment, and biological triplicates were examined for the injection control experiment reported in Figure S1.
These include the MIAME (Minimum Information about a Microarray Experiment) conventions for reporting microarray data, the CEBS Chemical Effectss in Biological Systems) database standards, and the developing SEND (Standard for Exchange of Nonclinical Data) standards for reporting preclinical safety data.
In the experiments reported here, all microarrays were printed in which an alien 70 mer probe was co-printed with the different gene specific probes such that the alien was at a final concentration of 10% of the murine gene oligonucleotides.
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