From: <Wang>, "Hsiao-Lin (UMKC-Student)" <hlwckf@mail.umkc.edu>
Date: Sunday, November 16, 2014 at 8:49 PM
To: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Subject: Some questions regarding tiling microarray on two different ecotypes of Arabidopsis thaliana

Hi, Ann,

I am Hsiao-Lin from Julia Chekanva's lab. I met you at the 2013 Genome informatics meeting in CSHL, and I attended the WINGS this year in May and gave a talk at the RCN meeting in Charlotte. It was a great opportunity to give my first talk and learn the packages that you and your student demonstrated during the workshop, they've been extremely useful!

I recently defended my dissertation and I am in the process of wrapping up several projects. One of them is to analyze the differentially expressed regions of our mutants using the Affymetrix Tiling Array chips (1.0R). This project was initially started by former post-doc, and we already have a collection of tiling array data of our mutants. I've not analyze array data before (my focus has been in smRNA-seq and RNA-seq). While I was readying various things, I came across one of your posting regarding the TAIR9 bpmap file (http://www.bio.net/mm/arabidopsis/2009-September/012138.html). You are experts in Arabidopsis genomics, and I have several questions and I am wondering if you could help me.

While majority of our mutants were in Col-0 background, several of them were in the Landsberg background; therefore, in additional to Col-0, we also have tiling array data of these mutants in Landsberg background using the 1.0R Affymetrix chip. I understand the probes on the 1.0R tiling array chip was designed using Col-0 genomic sequences, but is it possible to analyze the gene expression when the mutants are in Landsberg background using 1.0R chip? In another words, is it possible to use mismatch to pay pass the SNPs between two ecotypes? or if the SNPs between the two ecotypes are minimal and specific, perhaps I can just process them in the same way? or is there a standard/proper way to process these data so I can find the statistically sound and significantly differentially expressed regions (when they are Landsberg mutants)? Thank you, and I hope these questions are not too much trouble and I hope you don't mind to give me some suggestions or share your expertise.

Also, I truly appreciated the new IGB (it's very more friendly compared to the old version) : )

Thank you, and I am looking forward for your suggestions.

Cheers,

Hsiao-Lin.

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Hsiao-Lin Wang, Ph.D.

Dr. Julia Chekanova Laboratory
School of Biological Sciences
University of Missouri-Kansas City
hlwckf@mail.umkc.edu