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|Medicago truncatula Gene Expression Atlas|
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Microarray Sample Selection
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Downloading the mapping file
We have generated the mapping file for Gene IDs of Medicago IMGAG V3.5 vs Affymetrix probeset IDs usng the following mapping strategy. You may click here to download this excel mapping file.
For IMGAG V4.0 vs Affymetrix probeset IDs file, you can download here.
MGAG Gene to Affymetrix GeneChip Mapping Strategy
1. We aligned all probes (25 mer) against IMGAG genome sequences ver 3.5.3, based on BWA short sequence alignment, allowing maximally 5bp mismatch per probe.
2. For each IMGAG transcript model, we identified its start and end coordinates on the genome, and then searched the probes that are aligned to the same genomic region. If there were at least 4 distinct probes from a same probeset in that region, the IMGAG transcript ID – probeset ID mapping information would then be reported.
3. You will note some (partially) one-to-many, many-to-one, and potentially many-to-many mappings. In the Excel mapping file, we’ve given a few examples with our own interpretations. There will be many other cases not covered in our examples but we’d be happy to provide assistance if you want to track down the alignment details on some particular transcripts / probesets.
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