Dahlquist:SURP 2015 Schedule

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SURP 2015 Schedule

Week	Date	Wet Lab	GRNsight	GRNmap	Meetings & Events
1	Mon May 18	Work with GRNmap team	Work with GRNmap team	AM: How to wiki, PowerPoint overview PM: Within- and between-array normalization, one-strain ANOVA	All group members report to S120 for microarray data analysis Register for the OpenWetware Wiki if you haven't already
	Tues May 19	Work with GRNmap team	Work with GRNmap team	AM: Modified T test PM: Between-strain ANOVA, clustering with stem, preparation of GenMAPP input sheet, "Deception at Duke" video, "Baggerly: Forensic Bioinformatics" video, research ethics discussion	SURP BBQ, 12:00-1:00 PM, Bird's Nest
	Wed May 20	Work with GRNmap team Decide which strain to label and hybridize to microarrays: Δino2, Δopi1, or Δyap1 Decide which strains to test for growth impairment in cold: Δarg80, Δrsf2, Δrtg3, Δtbf1, Δyhp1, Δyox1, Δphd1, Δnrg1 or other	Work with GRNmap team	GenMAPP, YEASTRACT	Joint group meeting, 12:00-2:00 PM, S202 Nicole & Anu present journal club Shannon et al. (2003), Cytoscape Journal Club Presentation
2	Tues May 26	Work with GRNmap team	Work with GRNmap team; GRNsight code walk-through	All: Create input sheet and run GRNmap Tessa/Trixie: work on issue #74
	Wed May 27	AM: F1 cDNA synthesis PM: F1 cDNA purification, aRNA synthesis			GRNsight meeting 11:00-12:00 PM, S202 Joint group meeting, 12:00-2:00 PM, S202 Monica & Kevin W. present journal club Hebly et al. (2014) GRNmap meeting 2:00-3:00 PM, S202
	Thurs May 28	AM: F1 aRNA purification, quantification PM: F1 aRNA gel			Glenn Johnson-Grau: workshop on searching the literature Nicole's last day
3	Mon June 1	AM: dry F1 aRNA, F1 cDNA synthesis PM: F1 label & hybe
	Tues June 2	AM: F1 wash & scan PM: F2 cDNA purification, aRNA synthesis
	Wed June 3	AM: F2 aRNA purification, quantification PM: F2 aRNA gel			Joint group meeting, 12:00-2:00 PM, S202 Natalie & Kevin M. present journal club Geistlinger et al. (2013)
4	Mon June 8	AM: dry F2 aRNA, F3 cDNA synthesis PM: F2 label & hybe
	Tues June 9	AM: F2 wash & scan PM: F3 cDNa purification, aRNA synthesis
	Wed June 10	AM: F3 aRNA purification, quantification PM: F3 aRNA gel			Joint group meeting, 12:00-2:00 PM, S202 (Grace), Tessa, & Trixie present journal club Vu & Vohradsky (2007)
5	Mon June 15	AM: dry F3 aRNA, F4 cDNA synthesis PM: F3 label & hybe			(KD at BioQUEST workshop)
	Tues June 16	AM: F3 wash & scan PM: F4 cDNA purification, aRNA synthesis			(KD at BioQUEST workshop)
	Wed June 17	AM: F4 aRNA purification, quantification PM: F4 aRNA gel			Joint group meeting, 12:00-2:00 PM, S202 Brandon & (Grace) presents journal club Natalie's last day
6	Mon June 22	AM: PM: F4 label & hybe
	Tues June 23	AM: F4 wash & scan
	Wed June 24	Lab check-out	Lab check-out	Lab check-out	Joint group meeting, 12:00-2:00 PM, S202 Everyone gives final research presentations SURP Abstracts due to Undergraduate.Research@lmu.edu

Strain Voting

Δyap1

• Within-strain
  • 1, Katherine Grace Johnson 14:40, 20 May 2015 (EDT)
  • 2, Natalie Williams 14:44, 20 May 2015 (EDT)
  • 0, Tessa A. Morris 14:47, 20 May 2015 (EDT)
  • 1, Kevin Patrick McGee 14:50, 20 May 2015 (EDT)
  • 1, Kevin Wyllie 14:54, 20 May 2015 (EDT)
• Between-strain
  • 0, Katherine Grace Johnson 14:40, 20 May 2015 (EDT)
  • 2, Natalie Williams 14:44, 20 May 2015 (EDT)
  • 2, Tessa A. Morris 14:47, 20 May 2015 (EDT)
  • 0, Anindita Varshneya 14:49, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:50, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:54, 20 May 2015 (EDT)
• Total 5 + 4 = 9

Δino2

• Within-strain
  • 2, Katherine Grace Johnson 14:36, 20 May 2015 (EDT)
  • 1, Kevin Wyllie 14:39, 20 May 2015 (EDT)
  • 1, Natalie Williams 14:41, 20 May 2015 (EDT)
  • 1, Tessa A. Morris 14:48, 20 May 2015 (EDT)
  • 2, Kevin Patrick McGee 14:49, 20 May 2015 (EDT)
• Between-strain
  • 0, Katherine Grace Johnson 14:36, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:39, 20 May 2015 (EDT)
  • 0, Natalie Williams 14:41, 20 May 2015 (EDT)
  • 0, Anindita Varshneya 14:47, 20 May 2015 (EDT)
  • 0, Tessa A. Morris 14:48, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:49, 20 May 2015 (EDT)
• Total = 7 + 0 = 7

Δopi1

• Within-Strain
  • 1 Katherine Grace Johnson 14:39, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:40, 20 May 2015 (EDT)
  • 0, Natalie Williams 14:42, 20 May 2015 (EDT)
  • 0, Tessa A. Morris 14:47, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:50, 20 May 2015 (EDT)
• Between-Strain
  • 0, Kevin Patrick McGee 14:50, 20 May 2015 (EDT)
  • 0 Katherine Grace Johnson 14:39, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:40, 20 May 2015 (EDT)
  • 0, Natalie Williams 14:42, 20 May 2015 (EDT)
  • 0, Tessa A. Morris 14:47, 20 May 2015 (EDT)
  • 0, Anindita Varshneya 14:47, 20 May 2015 (EDT)
• Total 1 + 0 = 1

---

Δrtg3

• yeast box 1-78
• Within-strain
  • 0, Tessa A. Morris 14:45, 20 May 2015 (EDT)
  • 0, Katherine Grace Johnson 14:45, 20 May 2015 (EDT)
  • 2, Natalie Williams 14:49, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:50, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:51, 20 May 2015 (EDT)
• Between-strain ANOVA
  • 2, Kam D. Dahlquist 14:42, 20 May 2015 (EDT) (wt v. dZAP1)
  • 2, Tessa A. Morris 14:45, 20 May 2015 (EDT)
  • 2, Katherine Grace Johnson 14:45, 20 May 2015 (EDT)
  • 3, Natalie Williams 14:49, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:50, 20 May 2015 (EDT)
  • 0, Anindita Varshneya 14:51, 20 May 2015 (EDT)
  • 2, Kevin Patrick McGee 14:51, 20 May 2015 (EDT)
• Total = 2 + 11 = 13

Δrsf2

• yeast box 14-49
• Within-Strain ANOVA
  • 2, Katherine Grace Johnson 14:44, 20 May 2015 (EDT)
  • 0, Tessa A. Morris 14:45, 20 May 2015 (EDT)
  • 2, Natalie Williams 14:48, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:51, 20 May 2015 (EDT)
  • 2, Kevin Wyllie 14:52, 20 May 2015 (EDT)
• Between-strain ANOVA
  • 2, Kam D. Dahlquist 14:41, 20 May 2015 (EDT) (wt v. dZAP1)
  • 3, Katherine Grace Johnson 14:44, 20 May 2015 (EDT)
  • 0, Tessa A. Morris 14:45, 20 May 2015 (EDT)
  • 2, Natalie Williams 14:48, 20 May 2015 (EDT)
  • 0, Anindita Varshneya 14:51, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:51, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:52, 20 May 2015 (EDT)
• Total = 6 + 7 = 13

Δtbf1

• don't have
• Within-strain
  • 0, Tessa A. Morris 14:44, 20 May 2015 (EDT)
  • 0, Katherine Grace Johnson 14:46, 20 May 2015 (EDT)
  • 0, Natalie Williams 14:49, 20 May 2015 (EDT)
  • 2, Kevin Wyllie 14:50, 20 May 2015 (EDT)
  • 1, Kevin Patrick McGee 14:51, 20 May 2015 (EDT)
• Between-strain
  • 2, Kam D. Dahlquist 14:43, 20 May 2015 (EDT), (wt vs. dZAP1)
  • 0, Tessa A. Morris 14:44, 20 May 2015 (EDT)
  • 0, Katherine Grace Johnson 14:46, 20 May 2015 (EDT)
  • 3, Natalie Williams 14:49, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:50, 20 May 2015 (EDT)
  • 2, Kevin Patrick McGee 14:51, 20 May 2015 (EDT)
  • 2 Anindita Varshneya 14:53, 20 May 2015 (EDT)
• Total = 3 + 9 = 12

Δyox1

• box 1-59
• Within-strain
  • 1, Tessa A. Morris 14:41, 20 May 2015 (EDT)
  • 1, Kevin Wyllie 14:48, 20 May 2015 (EDT)
  • 2, Katherine Grace Johnson 14:49, 20 May 2015 (EDT)
  • 2, Natalie Williams 14:50, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:54, 20 May 2015 (EDT)
• Between-strain
  • 0, Tessa A. Morris 14:41, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:48, 20 May 2015 (EDT)
  • 0, Katherine Grace Johnson 14:49, 20 May 2015 (EDT)
  • 2, Natalie Williams 14:50, 20 May 2015 (EDT)
  • 2, Anindita Varshneya 14:53, 20 May 2015 (EDT)
  • 2, Kevin Patrick McGee 14:54, 20 May 2015 (EDT)
• Total = 6 + 6 = 12

Δyhp1

• box 10-14 or 11-81
• Within-strain
  • 0, Tessa A. Morris 14:42, 20 May 2015 (EDT)
  • 2, Katherine Grace Johnson 14:48, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:49, 20 May 2015 (EDT)
  • 0, Natalie Williams 14:50, 20 May 2015 (EDT)
  • 2, Kevin Patrick McGee 14:52, 20 May 2015 (EDT)
• Between-strain
  • 0, Tessa A. Morris 14:42, 20 May 2015 (EDT)
  • 0, Katherine Grace Johnson 14:48, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:49, 20 May 2015 (EDT)
  • 2, Natalie Williams 14:50, 20 May 2015 (EDT)
  • 2, Kevin Patrick McGee 14:52, 20 May 2015 (EDT)
  • 2, Anindita Varshneya 14:53, 20 May 2015 (EDT)
• Total = 4 + 6 = 10

Δphd1

• box 2-53
• Within-strain
  • 0, Tessa A. Morris 14:41, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:42, 20 May 2015 (EDT)
  • 1, Katherine Grace Johnson 14:50, 20 May 2015 (EDT)
  • 2, Natalie Williams 14:51, 20 May 2015 (EDT)
  • 1, Kevin Patrick McGee 14:54, 20 May 2015 (EDT)
• Between-strain
  • 0, Tessa A. Morris 14:41, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:42, 20 May 2015 (EDT)
  • 2, Katherine Grace Johnson 14:50, 20 May 2015 (EDT)
  • 3, Natalie Williams 14:51, 20 May 2015 (EDT)
  • 0, Anindita Varshneya 14:54, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:54, 20 May 2015 (EDT)
• Total = 4 + 5 = 9

Δnrg1

• box 2-3
• Within-strain
  • 2, Tessa A. Morris 14:40, 20 May 2015 (EDT)
  • 1, Kevin Wyllie 14:41, 20 May 2015 (EDT)
  • 2, Katherine Grace Johnson 14:51, 20 May 2015 (EDT)
  • 0, Natalie Williams 14:52, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:54, 20 May 2015 (EDT)
• Between-strain
  • 2, Tessa A. Morris 14:40, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:41, 20 May 2015 (EDT)
  • 2, Katherine Grace Johnson 14:51, 20 May 2015 (EDT)
  • 0, Natalie Williams 14:52, 20 May 2015 (EDT)
  • 0, Anindita Varshneya 14:54, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:54, 20 May 2015 (EDT)
• Total = 5 + 4 = 9

Δarg80

• box 2-16 or 2-74
• Within-strain
  • 0, Katherine Grace Johnson 14:41, 20 May 2015 (EDT)
  • 0, Tessa A. Morris 14:46, 20 May 2015 (EDT)
  • 0, Natalie Williams 14:47, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:50, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:53, 20 May 2015 (EDT)
• Between-strain
  • 0 Katherine Grace Johnson 14:41, 20 May 2015 (EDT)
  • 0, Tessa A. Morris 14:46, 20 May 2015 (EDT)
  • 0, Natalie Williams 14:47, 20 May 2015 (EDT)
  • 0, Anindita Varshneya 14:49, 20 May 2015 (EDT)
  • 0, Kevin Patrick McGee 14:50, 20 May 2015 (EDT)
  • 0, Kevin Wyllie 14:53, 20 May 2015 (EDT)
• Total 0 + 0 = 0