Details
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Type:
Support
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Labels:None
Description
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
Attachments
Issue Links
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DB-133 Respond to user's e-mail about tiling microarray data for A. thaliana ecoptypes
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- Open
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Activity
From: <Wang>, "Hsiao-Lin (UMKC-Student)" <hlwckf@mail.umkc.edu>
Date: Tue 11/18/2014 11:34 AM
To: Mason Meyer <Mason.Meyer@my.lr.edu>
Subject: Some questions regarding tiling microarray on two different ecotypes of Arabidopsis thaliana
Hello Mason,
Thank you. I am looking forward for the answer! : )
Thanks again.
Hsiao-Lin.
From: Mason Meyer <Mason.Meyer@my.lr.edu>
Date: Tue 11/18/2014 11:21 AM
To: <Wang>, "Hsiao-Lin (UMKC-Student)" <hlwckf@mail.umkc.edu>
CC: "Loraine, Ann" <Ann.Loraine@uncc.edu>, Nowlan Freese <nfreese@uncc.edu>
Subject: Some questions regarding tiling microarray on two different ecotypes of Arabidopsis thaliana
Hello Hsiao-Lin,
My name is Mason Meyer and I’m a user support specialist who is currently working on the IGB project. I wanted to let you know that we are happy to help you answer any questions you may have for us. We have added an issue to our queue so that we can dedicate time and focus on answering all of your questions very soon. Please look for an e-mail from us within the next week or so, and in the meantime, let us know if you have any additional questions. Thanks again for contacting us!
Thanks again,
Mason Meyer