Summer Research 2009Functional Genomics Research Stream • Freshman Research Initiative • by Dr. Patrick J. Killion

Summer 2009 - Functional Genomics Research Stream

Introduction

Welcome to the summer research portion of the Freshman Research Initiative Functional Genomics Research Stream.

This will be an exciting next step in your growth progress as a researcher. You have emerged from the spring semester well trained and ready for difficult molecular protocols. We will focus on hard problems this summer. Additionally, we will spend significant time discussing literature in order to better acquaint you with the research we are pursuing and the practice of reading scientific literature in general.

Dates & Hours

Research will run from roughly June 1 until August 1.

Each of you are working different hours depending on how you are being funded. We will track hours the same way we did during the semester (using the sign-in sheets). I expect you to be thorough in your use of these sheets and adhere to a high code of honor with respect to the hours that you report.

My expectations for hours in the laboratory are the following.

Mentors Not on Fellowship: ~ 10 Hours per Week

Mentors & Students on Fellowship: Total of 160 Hour Commitment (20 x 8), ~ 20 Hours per Week

Research Volunteers: ~ 10 Hours per Week

I expect that each of you will have fulfilled nearly ½ your expected hours by July 1. You will need to speak with me if you find this to not be possible. Finally, the lab will have an open policy with a key posted. Under NO CIRCUMSTANCES should you ever be in the lab alone. You must arrange parter work during nonstandard hours.

Expectations

I expect for everyone to operate as a professional during the course of the summer. We will have fun; professionals can have fun. That said, I need you to engaged in focused, heads-down work when you have goals to work to be done. I do not want to see or hear of significant experimental loss due to lack of focus or paying attention. I expect that you will keep on track with your hours and maintain a reasonable external academic schedule. Remember, you made a commitment by accepting this fellowship and it is your professional responsibility to honor that commitment. I expect you to own your work - both literally and philosophically. Finally, I expect that you will productively and collegially interact with your peers. You will produce a short report at the end of the summer detailing your work. Details will be provided nearer that date.

I understand the hours and expectations stated above and agree to them.

Signed: _______________________________________________ Date: _______________

Google Lab Calendar

The lab PAI 2.46 has a Google account dedicated to it for its operations and scheduling.

Go to: http://www.gmail.com/

Username: fripai246Password: <see me>

* Please keep this username and password confidential and DO NOT send email from this account for any purpose.

Click “Calendar”

Please note that you can and should schedule:

• BENCH 1-8• GEL 1-7• LAPTOP 1-2• PCR 1-2

Table of Contents

The following is the information provided in your summer research packet. Please have this packet with you at all times in the lab. You are encouraged to take it with you for reading but please always bring it to lab.

Program Content

Freshman Research Initiative - Summer Fellowship Orientation Meeting Notes

Lecture Slides

May 5, 2009 - The Road to Publication

Textbook Chapters

Unit 3.1 - Reagent Preparation: Theoretical and Practical Discussion

Unit 4.1 - Aseptic Technique

Unit 5.2 - Purification and Concentration of Nucleic Acids

Protocols

From Methods in Yeast Genetics - 2005 Edition:

Yeast DNA Isolations

Yeast RNA Isolations

Cell Synchrony

Chromatin Immunoprecipitation

From Short Protocols in Molecular Biology:

Characterization of Proteins Bound to Chromatin by Immunoprecipitation from Whole-Cell Extracts

From Cold Spring Harbor Protocols:

Yeast Chromatin Immunoprecipitation (ChIP) Assay

From Iyer Lab:

Yeast Chromatin Immunoprecipitation (ChIP)

From Open Biosystems:

Yeast TAP-Fusion Library

Papers

Spellman et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell (1998) vol. 9 (12) pp. 3273-97

Iyer et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature (2001) vol. 409 (6819) pp. 533-8

Simon et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell (2001) vol. 106 (6) pp. 697-708

Massie and Mills. ChIPping away at gene regulation. EMBO Rep (2008) vol. 9 (4) pp. 337-43

Lefrançois et al. Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) vol. 10 pp. 37

Wold and Myers. Sequence census methods for functional genomics. Nat. Methods (2008) vol. 5 (1) pp. 19-21

Shendure and Ji. Next-generation DNA sequencing. Nat Biotechnol (2008) vol. 26 (10) pp. 1135-45

Wilhelm et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) vol. 453 (7199) pp. 1239-43

Nagalakshmi et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) vol. 320 (5881) pp. 1344-9

Borneman et al. Divergence of transcription factor binding sites across related yeast species. Science (2007) vol. 317 (5839) pp. 815-9

Jiang and Pugh. Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet (2009) vol. 10 (3) pp. 161-72