I. Array Design Description In this study, a commercially available 5000 rat oligonucleotide array (CAG, ICPH, Newark, NJ) was employed. Please refer to the websites www.cag.icph.org and www.ngelab.org about the detailed array design elements.
The following information was required by the MGED: 1. Array related information: array design name: Rat 5K Oligo Array (NGEL 2.01); platform type: spotted; surface and coating specification: flat, silicon coating; physical dimensions of array support: glass slide; number of features on the array: about 5000; availability: commercial arrays. 2. a) For each reporter type: single stranded synthetic 60-70 base oligo- nuceotides. b) For each reporter: sequence, lengths, and element generation protocol information: please require from manufacturer or refer to its website. 3. a) For each feature type: dimensions. b) For each feature: refer to the manufacturer's website. 4. For each composite sequence: refer to the manufacturer's website. 5. Control elements on the array: position of the feature: refer to the manufacturer's website; control type: negative and positive; control qualifier: endogenous.
The Neuroscience Gene Expression Laboratory (NGEL) 2.01 Rat Oligo arrays were purchased from the Center for Applied Genomics (CAG), International Center for Public Health (ICPH), Newark, NJ. The arrays are mainly built from two groups of oligonucleotides: the complete Compugen C-GEN Rat library (4,854 oligos representing 4,803 independent genes and over 9,225 independent mRNAs) and a custom-designed set based on suggestions from our collaborators (approximately 120 oligos). The total gene number is about 5000, so it is also called 5 k rat oligo array. All oligos are 60-70 nt, and are 5' amine linked to aldehyde modified slides. The array also contains a number of custom-designed controls, including random sequence negative probe, random sequence matching a Cy3-labeled complement positive control, common rat pathogen sequences, green fluorescent protein gene probe and a scale of 8:1 to 1:8 molar ratios of Genisphere capture sequences.
This array contains the Compugen C-GEN Rat library, as well as over 100 custom-synthesized rat probes.
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