GCAT-SEEKquence
The Genome Consortium for Active Teaching
NextGen Sequencing Group
NextGen Sequencing Request Form
Complete fields below, save file with your last name at the beginning of
the filename (e.g. newman-GCAT-SEEK Sequence request form.pdf) and
email to Vincent Buonaccorsi <BUONACCORSI@juniata.edu>
A. Contact Information
1. Name:
Nick Kaplinsky
2. Department: Biology
3. Institution: Swarthmore College
4. Phone Number: 610.328.8039
5. Email Address: nkaplin1@swarthmore.edu
B. Project Information
1. Title: Simultaneous mapping and cloning of a NudC modifier in Arabidopsis thaliana
2. Category: Sequencing based mapping and cloning
3. Total amount of sequence requested: 8Gb
4. Preferred technology: Illumina (1 land of 50bp single end Hiseq would do)
5. Do you have funds for a partial run next Spring? Yes
C. Describe the background, hypotheses and specific aims (500 words max)
BOB1 is an Arabidopsis small heat shock protein (sHSP) with functions in both development and
thermotolerance. We are interested in understanding how a sHSP affects development. My lab has identified
several BOBBER1 (BOB1) modifiers which we would like to clone. Last year we used a NGS simultaneous
mapping and cloning approach (SHOREmap from the Weigel lab) to clone our first modifier. We are now ready
to clone several more and would like to take a similar approach.
D. Describe the methods [sample prep, calculation of amount of sequence required, analysis plan]
Sample prep is a pooled DNA sample from 500 mutant plants in a mapping population (we use a Quiagen
plant maxi-kit). Illumina library preparation was performed using the standard Illumina protocol. We used
~8Gb of sequence for this approach last time although it would work with half of that. Analysis was
performed using SHOREmap (http://www.nature.com/nmeth/journal/v6/n8/full/nmeth0809-550.html) here
at Swarthmore. We have the expertise and computers required for the analysis.
E. Describe the role and number of undergraduates involved in the project, and how they would benefit.
This project would support a single honors research student. She would benefit by having her gene cloned and
could then spend her remaining time characterizing the gene. Apart from the cloning the sequence would be
very valuable for future students. We would be in a position to generate a very detailed resequenced genome of
the genetic background that we are working in which would make future cloning projects easier.
In the past I have folded my research into my teaching labs so it is possible that I could develop a lab involving
the use of these data for my intermediate Plant Biology course (24 students per year).
F. I agree to administer the GCAT-SEEK pre- and post-activity assessment test for students and to complete the
faculty post-utilization survey. __X__ yes, ____ no
G. Describe any other broader impact or intellectual merit considerations.
The more of these projects I do the better I get at teaching students how to do them.
H. References
Included above.