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Using MapMan

Mapping file for tomato Agilent 4X44 microarrays

I´m new at Mapman and have a dataset from Agilent microarrays. Is there a mapping file for this platform

Otherwise, any advice on how to use the other mapping files available for tomato?

Many thanks,

Arantza Rico

RE: Mapping file for tomato Agilent 4X44 microarrays
Answer
5/19/10 12:32 PM as a reply to Arantza Rico.
Dear Arantza,

unfortunately we do not yet have a mapping for the agilent tomato chip. If you supply a file
that contains that contains the probe sequences and/or a file that contains the target sequences we can
create a mapping and make it available online.

best greetings,
Marc

RE: Mapping file for tomato Agilent 4X44 microarrays
Answer
6/7/10 11:49 AM as a reply to Marc Lohse.
Dear Marc

I´m sorry I didn´t reply earlier

I have the GAL file that comes with the Agilent CDrom

Would that do? The GAL file contains information about each probe. The description of each probe is obtained from three different databases: GeneBank (GB accessions), TIGR (TA accessions: transcript assemblies, from EST clones) and the Tomato Gene Index (TC accessions: Tentative conseensus sequences from EST clones). Originally the GAL file only gave the description from GeneBank, but that left many unknowns in the data set, so we included several columns with descriptions from the other two databases.

I attach a txt file so you can check if that would be useful. It contains all the probes from the 4X44 chips with the results from one of my experiments

Many thanks,

Arantza Rico

RE: Mapping file for tomato Agilent 4X44 microarrays
Answer
6/9/10 10:10 AM as a reply to Arantza Rico.
Dear Arantza,

i fear the file you attached does not contain the information we'd need to create a mapping. If you supply the
probe sequences i can create a mapping based on the current SGN unigene release.

Best greetings,
Marc

RE: Mapping file for tomato Agilent 4X44 microarrays
Answer
6/11/10 11:34 AM as a reply to Marc Lohse.
Dear Marc,

I'm trying to get that file with the probe sequences from our collaborators, who purchased and performed the microarrays. How would be the best way to send it to you?

Best wishes, and many thanks for your help

Arantza

RE: Mapping file for tomato Agilent 4X44 microarrays
Answer
6/15/10 12:01 PM as a reply to Marc Lohse.
Dear Marc

I found the file with the probe sequences in the Agilent website (eArray utility).

I attach the document as a text file separated by tabs. I hope it is the one you need. Please let me know if you need anything else and many thanks in advance

Best wishes,

Arantza Rico

RE: Mapping file for tomato Agilent 4X44 microarrays
Answer
6/15/10 12:09 PM as a reply to Arantza Rico.
Dear Arantza,

with this file i can do the crossmapping - i will notify you as soon as the mapping is finished.

best greetings,
Marc

RE: Mapping file for tomato Agilent 4X44 microarrays
Answer
6/15/10 12:44 PM as a reply to Marc Lohse.
Thanks so much!

RE: Mapping file for tomato Agilent 4X44 microarrays
Answer
6/15/10 2:31 PM as a reply to Arantza Rico.
Dear Arantza,

the crossmapping is finished. I am not sure whether the platform you used is publically available or your
private design. If it's public i will upload the mapping to the public MapManStore webpage (http://mapman.gabipd.org/web/guest/mapmanstore).
In case it's private, please supply an e.g. email adress i can send the file to.

cheers,
Marc

RE: Mapping file for tomato Agilent 4X44 microarrays
Answer
6/16/10 1:20 PM as a reply to Marc Lohse.
Dear Marc,

We purchased the microarrays from Agilent

http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/tomatooligomicroarraykit/Pages/default.aspx

The sequences I sent you were available in the Agilent website (eArray) as long as you registered in the service (It is also used to design your own arrays to order them to Agilent). There was no need to pay for those files, so I guess you could upload it to the Mapman website.

If you're not sure about it, please send the file to this email address:

aran.rico@gmail.com

Thanks,

Arantza

RE: Mapping file for tomato Agilent 4X44 microarrays
Answer
6/17/10 7:51 PM as a reply to Arantza Rico.
Dear Arantza,

thank you for the information. Since we have made other mappings that were create based on the sequences provided
by AGILENT publicly available, i will proceed the same way with your mapping. Please check the MapManStore website
to find the new mapping file.

http://mapman.gabipd.org/web/guest/mapmanstore

Best greetings,
Marc