How to conveniently get the sequence of probes from the GPL annotation Data table in GEO

Question

[Zhilong Jia]

In the data table of some platform annotation (like http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL341), there is no sequence information, though there is sequence information in some platforms. That's because the only truth in the platform annotation is the probe sequence. Others will change with the time due to the genome annotation update. So, it's preferable to get the annotation from the probe sequence directly. The problem here is how to conveniently obtain the sequence of probes. Any suggestion? Thank you.

Answer 1

[Sean Davis]

There is no general answer to your question. In fact, some microarray manufacturers did not make the probe sequences available. For any particular microarray platform, you'll need to investigate with the manufacturer or submitter how best to get the probe sequence.

[Zhilong Jia]

@SeanDavis Nice to see you again. In 2005, people have noticed that Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. And there are other tools, like AILUN, annotating GPL with probe_ID or Gene/Clone/Protein ID, but they have not used the probe sequence. Ten years later, the problem does not been solved. For RNA-Seq, people prefer to map the raw data to the updated genome annotation by themselves and this situation could occur for microarray data, too. To investigate with the manufacturer or submitter of all GPLs is unreality at least for me. I hope there are other solution to cope with this problem. Thank you.

[Sean Davis]

NCBI GEO simply reports what submitters have provided. There is no process in place to gather "more information" than that. That leaves the search for information not in GEO up to the individual investigator, unfortunately.