PubMed · 15948319
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2005. Consolidating genetic data.. https://doi.org/10.1016/s1470-2045(05)70177-7
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Members of the International Nucleotide Sequence Database Collaboration (INSDC; https://www.insdc.org/) collect, exchange, and preserve comprehensive open nucleotide sequence information and provide tools for its access. The INSDC has stated its commitment to welcoming new members into the collaboration to be more representative of the global community of data and users. To reach this goal, a comprehensive definition of the INSDC data model and minimum requirements for data acceptance have been established. Here we describe the processes used to arrive upon these INSDC Specifications and lay out strategies for their continued upkeep to remain current and relevant. Database URL:  https://www.insdc.org/.
BACKGROUND: There are many potential sources of variability in a microarray experiment. Variation can arise from many aspects of the collection and processing of samples for gene expression analysis. Oligonucleotide-based arrays are thought to minimize one source of variability as identical oligonucleotides are expected to recognize the same transcripts during hybridization. RESULTS: We demonstrate that although the probes on the U133A GeneChip arrays are identical in sequence to probes designed for the U133 Plus 2.0 arrays the values obtained from an experimental hybridization can be quite different. Nearly half of the probesets in common between the two array types can produce slightly different values from the same sample. Nearly 70% of the individual probes in these probesets produced array specific differences. CONCLUSION: The context of the probe may also contribute some bias to the final measured value of gene expression. At a minimum, this should add an extra level of caution when considering the direct comparison of experiments performed in two microarray formats. More importantly, this suggests that it may not be possible to know which value is the most accurate representation of a biological sample when comparing two formats.
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