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NimbleGen provides a complete suite of microarray design services, including experimental design consultation, DNA sequence quality control, optimal probe selection, and microarray layout and design. This expertise, in conjunction with the underlying Maskless Array Synthesizer (MAS) technology, provides ultimate flexibility in quickly and iteratively designing arrays to fine-tune results.
NimbleGen's team of scientists and bioinformatics specialists bring years of experience to your experiment. You have the option to provide NimbleGen with a list of probes for your model organism, or our team can help you select target sequences, acquire target sequence data, select optimal probes, and design an array.
NimbleGen scientists perform consistency checks on the target sequence data, including removing pseudo-genes, testing sequences for proper start codons, screening internal stop codons within coding regions, removing redundant sequences, and retrieving the highest quality sequence data available from public sequence data sources.
NimbleGen selects optimal probes from your genome of interest using a proprietary probe screening system developed exclusively for the MAS platform. Probe sets are selected which uniquely represent the genomic target or gene transcripts of interest, and which are predicted to have excellent hybridization characteristics. Our predictive software is based on a combination of NimbleGen's innovative Tm-balanced probe selection coupled with heuristic and AI predictive methods derived from a growing volume of experimental data. For each new design, NimbleGen can provide you with a QC summary of each probe listing the details of all of our scoring criteria.
The final step in the design process is the creation of "digital masks," or electronic files that control the patterning of the micromirrors in the Maskless Array Synthesizer (MAS) during the array manufacture.
All arrays include a number of reference probes, which aid in identifying the edges of the array and help in aligning a reference grid when extracting intensity values from the scanned image of the array. NimbleGen arrays also include a number of standards,distributed throughout the array. These include both concentration standards (spiked-in oligos at known concentrations) and NimbleGen's synthesis efficiency standards. Additional controls encoded within the DNA array to provide additional process and tracability controls.
Unlike traditional arrays, which require physical photolithographic masks, NimbleGen offers the ultimate flexibility in microarray design with "digital masks." These digital masks, one shown here with a zoom window, can be easily modified in little time and with little cost involved.
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