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The development of DNA microarray assays is hampered by two important aspects: processing of the microarrays is done under a single stringency condition, and characteristics such as melting temperature are difficult to predict for immobilized probes.
As a comparison, M197 sequence recognized by KLF4 in the protein microarray assays is shown below.
It should be noted that, while they provide a means to survey transcript abundance on a genome-wide scale, the sensitivity of microarray assays is low compared to other approaches such as real-time PCR.
More detailed explanation of microarray assays is provided in Additional file 1. Ingenuity Pathway Analysis 8.5 (IPA) (Ingenuity Systems, Redwood City, CA, USA) was used to select, annotate and visualize genes by function and pathway (gene ontology).
Although the field of microarray assays is still in a relatively early stage, it is generally anticipated that microarray assays will offer decreased cost and faster results, compared with the traditional, more labor intensive dideoxy sequencing approach.
Due to the fact that the cost of microarray assays is directly proportionate to the number of probes included, it is ideal to design the assay with the minimal number of probes necessary in order to minimize cost and increase the ease in analyzing the assay results.
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TaqMan assays were run for 48 genes on each of the 5 RNA samples that were used in microarray and RNA-seq assays.
All microarray data is MIAME compliant.
Microarray data is compliant with MIAME protocol.
The microarray platform is Affymetrix ATH1 GeneChip.
Microarray data is available at http://www.arexdb.org.
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