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 Anu/Natalie: wt Grace/Monica: Δhap4 Kevin M./Nicole: Δgln3 Kevin W./KD: Δswi4 Tessa/Trixie:Δcin5 Note that we chose not to do Δhmo1, Δzap1 or S. paradoxus so that students could work in pairs and check each others' work.	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 (voted no), Δrsf2, Δrtg3, Δtbf1 (essential, null not available), 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 TM/TR: work on issue #74
	Wed May 27	MH/KW: Δyap1 F1 cDNA synthesis, Δyap1 F1 cDNA purification, aRNA synthesis KM: genotyping PCR Δnrg1			GRNsight meeting 11:00-12:00 PM, S202 Joint group meeting, 12:00-2:00 PM, S202 Monica & Kevin W. present journal club Kevin and Monica's journal club Powerpoint; 05/27/2015 Hebly et al. (2014) GRNmap meeting 2:00-4:00 PM, S202
	Thurs May 28	MH/KW: repeat Δyap1 F1 cDNA synthesis, Δyap1 F1 cDNA purification KM: Δnrg1 PCR gel, Δphd1 genotyping PCR		GJ/NW: work on issue #10	1:00 PM, S120, Glenn Johnson-Grau: workshop on searching the literature BIOL478 Annotated Bibliography Assignment BIOL478 LibGuide BIOL368 Annotated Bibliography Assignment BIOL368 LibGuide BIOL367 LibGuide Nicole's last day
3	Mon June 1	MH/KW: Δyap1 F1 aRNA synthesis, purification, A260 KM: Δnrg1, Δphd1 temp-sensitive growth expt on plates
	Tues June 2	MH/KW: Δyap1 F1 aRNA gel, dry samples KM: repeat Δphd1 PCR w/wt template; PCR Δrsf2
	Wed June 3				GRNsight meeting 11:00-12:00 PM, S202 Joint group meeting, 12:00-2:00 PM, S202 Natalie & Kevin M. present journal club Geistlinger et al. (2013) Media:KM NW Journal Club CGRNds.pptx GRNmap meeting 2:00-4:00 PM, S202
4	Mon June 8	KM: Δrsf2, Δrtg3 temp-sensitive growth expt on plates
	Tues June 9
	Wed June 10				GRNsight meeting 11:00-12:00 PM, S202 Joint group meeting, 12:00-2:00 PM, S202 Grace, Tessa, & Trixie present journal club Vu & Vohradsky (2007) Yip et al. (2010) GRNmap meeting 2:00-4:00 PM, S202
5	Mon June 15	KM: Δyhp1, Δyox1 temp-sensitive growth expt on plates			(KD at BioQUEST workshop)
	Tues June 16				(KD at BioQUEST workshop)
	Wed June 17				GRNsight meeting 11:00-12:00 PM, S202 Joint group meeting, 12:00-2:00 PM, S202 Brandon presents journal club Chiu et al. (2012) GRNmap meeting 2:00-4:00 PM, S202 Natalie's last day
6	Mon June 22
	Tues June 23
	Wed June 24	Lab check-out	Lab check-out	Lab check-out	Joint group meeting, 12:00-2:00 PM, S202 Group presentation for President Snyder Individual presentations SURP Abstracts due to Undergraduate.Research@lmu.edu Grace & Natalie's Abstract Anu's Abtract Tessa & Trixie's Abstract Kevin M., Kevin W., and Monica's Abstract

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; essential gene, strain not available
• 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