Hi,
Can I use Nimblegen Populus expression array for construction of pathways. I have expression data in .pair files. Are they compatible with MAPMAN software.
Thanks
Dhiraj

Hi Dhiraj,

to-date, we do not provide a mapping for the NimbleGen populus chip platform. But we'd be happy to provide one
in future to enable you and others using this chip to use MapMan and PageMan to analyse thier data. To generate
such a mapping of the NimbleGen probeset identifiers to MapMan Bins, we need either the target sequnecs (meaning the
sequences of the genes the probesets were designed to match) or at least the probe sequences for each probe in the
probesets (best would be both). It seems like NimbleGen does not provide this information readily on their webpage (at least
i could not find it) - so if you can provide the info to us or point us to the right webpage i'd be happy to generate a mapping
provided there are no license issues prohibiting that.

best greetings,
Marc

Hi Marc,

Sorry for the late response to your suggestions.
I have attached Nimblegen microarray design file.

080401_Populus_385K.ndf (Zipped file). This file contains the complete information about the probes, including sequences, target genes, and location in the array)
This file is really big in size.It's difficult to attach here.
080401_Populus_385K_Block.ngd (Zipped files). This file contains information on the target genes, including database source, gene name, gene accession number, and gene ID.)


Thanks for your help.

Dhiraj

Hi Dhiraj,

your post is missing the ndf file attachment. The probe sequences (hopefully) included in this
file could be used to generate a mapping based on the JGI poplar release mapping that is already
available. Taking this approach would be much faster than collecting all the hit sequences listed in
the ngd file and running them through our (currently heavily booked) automatic annotation pipeline.
Hence it would be great if you could supply the ndf file.

best greetings,
Marc

Hi Marc,
The ndf file is large in size. After zipping, it is 25MB. I tried attaching here in this message. It won't take it. Would it be fine, if I send you on your email account by another website.
Please let me know.

Thanks
Dhiraj

Hi Dhiraj,

try sending it to lohse<at>mpimp-golm.mpg.de - this account should be able to
receive large attachments. If this still fails do not hesitate to contact me again and
we'll find a different solution.

cheers,
Marc

Hi - i received your file and it appears to contain the information i need to do the
crossmapping to the JGI release. I will get back to you as soon as i have the
mapping ready for you.

Bests,
Marc

Hi Marc,

Thanks for such quick response.

Dhiraj

Hi Marc,

I was just wondering whether you need raw data file (microarray data) for testing them in your mapping file of Populus Nimblegen array. I have couple of raw data file which I can share with you.
I really appreciate your help.

Thanks

Dhiraj