Dahlquist:SURP 2015 Schedule: Difference between revisions

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** Nicole & Anu present journal club
** Nicole & Anu present journal club
** [http://genome.cshlp.org/content/13/11/2498.full Shannon et al. (2003)], [http://www.cytoscape.org/ Cytoscape]
** [http://genome.cshlp.org/content/13/11/2498.full Shannon et al. (2003)], [http://www.cytoscape.org/ Cytoscape]
** [[Media:NA_AV_Journal_Club.pptx | Journal Club Presentation]]
|--
|--
| '''2'''
| '''2'''
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* SURP Abstracts due to [mailto:Undergraduate.Research@lmu.edu Undergraduate.Research@lmu.edu]
* SURP Abstracts due to [mailto:Undergraduate.Research@lmu.edu Undergraduate.Research@lmu.edu]
|}
|}


== Strain Voting ==
== Strain Voting ==
Line 249: Line 249:
**0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:48, 20 May 2015 (EDT)
**0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:48, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:49, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:49, 20 May 2015 (EDT)
=== ''Δopi1''===
=== ''Δopi1''===
*Within-Strain
*Within-Strain
Line 270: Line 271:
**0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:47, 20 May 2015 (EDT)
**0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:47, 20 May 2015 (EDT)
**1, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:50, 20 May 2015 (EDT)
**1, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:50, 20 May 2015 (EDT)
**1, [[User:Kevin Wyllie|Kevin Wyllie]] 14:54, 20 May 2015 (EDT)
*Between-strain
*Between-strain
**0, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:40, 20 May 2015 (EDT)
**0, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:40, 20 May 2015 (EDT)
Line 276: Line 278:
**0, [[User:Anindita Varshneya|Anindita Varshneya]] 14:49, 20 May 2015 (EDT)
**0, [[User:Anindita Varshneya|Anindita Varshneya]] 14:49, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:54, 20 May 2015 (EDT)


=== ''Δarg80''===
=== ''Δarg80''===
Line 283: Line 286:
**0, [[User:Natalie Williams|Natalie Williams]] 14:47, 20 May 2015 (EDT)
**0, [[User:Natalie Williams|Natalie Williams]] 14:47, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:53, 20 May 2015 (EDT)
*Between-strain
*Between-strain
**0 [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:41, 20 May 2015 (EDT)
**0 [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:41, 20 May 2015 (EDT)
Line 289: Line 293:
**0, [[User:Anindita Varshneya|Anindita Varshneya]] 14:49, 20 May 2015 (EDT)
**0, [[User:Anindita Varshneya|Anindita Varshneya]] 14:49, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:53, 20 May 2015 (EDT)


=== ''Δrsf2''===
=== ''Δrsf2''===
Line 296: Line 301:
**2, [[User:Natalie Williams|Natalie Williams]] 14:48, 20 May 2015 (EDT)
**2, [[User:Natalie Williams|Natalie Williams]] 14:48, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:51, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:51, 20 May 2015 (EDT)
**2, [[User:Kevin Wyllie|Kevin Wyllie]] 14:52, 20 May 2015 (EDT)
* Between-strain ANOVA
* Between-strain ANOVA
** 2, [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 14:41, 20 May 2015 (EDT) (wt v. dZAP1)
** 2, [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 14:41, 20 May 2015 (EDT) (wt v. dZAP1)
Line 303: Line 309:
**0, [[User:Anindita Varshneya|Anindita Varshneya]] 14:51, 20 May 2015 (EDT)
**0, [[User:Anindita Varshneya|Anindita Varshneya]] 14:51, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:51, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:51, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:52, 20 May 2015 (EDT)


=== ''Δrtg3''===
=== ''Δrtg3''===
Line 310: Line 317:
**2, [[User:Natalie Williams|Natalie Williams]] 14:49, 20 May 2015 (EDT)
**2, [[User:Natalie Williams|Natalie Williams]] 14:49, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:51, 20 May 2015 (EDT)
* Between-strain ANOVA
* Between-strain ANOVA
** 2, [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 14:42, 20 May 2015 (EDT) (wt v. dZAP1)
** 2, [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 14:42, 20 May 2015 (EDT) (wt v. dZAP1)
Line 317: Line 325:
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:50, 20 May 2015 (EDT)
**0, [[User:Anindita Varshneya|Anindita Varshneya]] 14:51, 20 May 2015 (EDT)
**0, [[User:Anindita Varshneya|Anindita Varshneya]] 14:51, 20 May 2015 (EDT)
**2, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:51, 20 May 2015 (EDT)


=== ''Δtbf1''===
=== ''Δtbf1''===
Line 324: Line 333:
**0, [[User:Natalie Williams|Natalie Williams]] 14:49, 20 May 2015 (EDT)
**0, [[User:Natalie Williams|Natalie Williams]] 14:49, 20 May 2015 (EDT)
**2, [[User:Kevin Wyllie|Kevin Wyllie]] 14:50, 20 May 2015 (EDT)
**2, [[User:Kevin Wyllie|Kevin Wyllie]] 14:50, 20 May 2015 (EDT)
**1, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:51, 20 May 2015 (EDT)
*Between-strain
*Between-strain
** 2, [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 14:43, 20 May 2015 (EDT), (wt vs. dZAP1)
** 2, [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 14:43, 20 May 2015 (EDT), (wt vs. dZAP1)
Line 330: Line 340:
**3, [[User:Natalie Williams|Natalie Williams]] 14:49, 20 May 2015 (EDT)
**3, [[User:Natalie Williams|Natalie Williams]] 14:49, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:50, 20 May 2015 (EDT)
**2, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:51, 20 May 2015 (EDT)
**2 [[User:Anindita Varshneya|Anindita Varshneya]] 14:53, 20 May 2015 (EDT)


=== ''Δyhp1''===
=== ''Δyhp1''===
Line 337: Line 349:
** 0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:49, 20 May 2015 (EDT)
** 0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:49, 20 May 2015 (EDT)
**0, [[User:Natalie Williams|Natalie Williams]] 14:50, 20 May 2015 (EDT)
**0, [[User:Natalie Williams|Natalie Williams]] 14:50, 20 May 2015 (EDT)
**2, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:52, 20 May 2015 (EDT)
*Between-strain
*Between-strain
**0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:42, 20 May 2015 (EDT)
**0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:42, 20 May 2015 (EDT)
Line 342: Line 355:
** 0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:49, 20 May 2015 (EDT)
** 0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:49, 20 May 2015 (EDT)
**2, [[User:Natalie Williams|Natalie Williams]] 14:50, 20 May 2015 (EDT)
**2, [[User:Natalie Williams|Natalie Williams]] 14:50, 20 May 2015 (EDT)
**2, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:52, 20 May 2015 (EDT)
**2, [[User:Anindita Varshneya|Anindita Varshneya]] 14:53, 20 May 2015 (EDT)


=== ''Δyox1''===
=== ''Δyox1''===
Line 349: Line 364:
**2, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:49, 20 May 2015 (EDT)
**2, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:49, 20 May 2015 (EDT)
**2, [[User:Natalie Williams|Natalie Williams]] 14:50, 20 May 2015 (EDT)
**2, [[User:Natalie Williams|Natalie Williams]] 14:50, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:54, 20 May 2015 (EDT)
*Between-strain
*Between-strain
**0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:41, 20 May 2015 (EDT)
**0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:41, 20 May 2015 (EDT)
Line 354: Line 370:
**0, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:49, 20 May 2015 (EDT)
**0, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:49, 20 May 2015 (EDT)
**2, [[User:Natalie Williams|Natalie Williams]] 14:50, 20 May 2015 (EDT)
**2, [[User:Natalie Williams|Natalie Williams]] 14:50, 20 May 2015 (EDT)
**2, [[User:Anindita Varshneya|Anindita Varshneya]] 14:53, 20 May 2015 (EDT)
**2, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:54, 20 May 2015 (EDT)


=== ''Δphd1''===
=== ''Δphd1''===
Line 361: Line 379:
**1, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:50, 20 May 2015 (EDT)
**1, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:50, 20 May 2015 (EDT)
**2, [[User:Natalie Williams|Natalie Williams]] 14:51, 20 May 2015 (EDT)
**2, [[User:Natalie Williams|Natalie Williams]] 14:51, 20 May 2015 (EDT)
**1, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:54, 20 May 2015 (EDT)
*Between-strain
*Between-strain
**0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:41, 20 May 2015 (EDT)
**0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:41, 20 May 2015 (EDT)
Line 366: Line 385:
**2, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:50, 20 May 2015 (EDT)
**2, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:50, 20 May 2015 (EDT)
**3, [[User:Natalie Williams|Natalie Williams]] 14:51, 20 May 2015 (EDT)
**3, [[User:Natalie Williams|Natalie Williams]] 14:51, 20 May 2015 (EDT)
**0, [[User:Anindita Varshneya|Anindita Varshneya]] 14:54, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:54, 20 May 2015 (EDT)


=== ''Δnrg1''===
=== ''Δnrg1''===
Line 371: Line 392:
**2, [[User:Tessa A. Morris|Tessa A. Morris]] 14:40, 20 May 2015 (EDT)
**2, [[User:Tessa A. Morris|Tessa A. Morris]] 14:40, 20 May 2015 (EDT)
**1, [[User:Kevin Wyllie|Kevin Wyllie]] 14:41, 20 May 2015 (EDT)
**1, [[User:Kevin Wyllie|Kevin Wyllie]] 14:41, 20 May 2015 (EDT)
**2, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:51, 20 May 2015 (EDT)
**0, [[User:Natalie Williams|Natalie Williams]] 14:52, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:54, 20 May 2015 (EDT)
*Between-strain
*Between-strain
**2, [[User:Tessa A. Morris|Tessa A. Morris]] 14:40, 20 May 2015 (EDT)
**2, [[User:Tessa A. Morris|Tessa A. Morris]] 14:40, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:41, 20 May 2015 (EDT)
**0, [[User:Kevin Wyllie|Kevin Wyllie]] 14:41, 20 May 2015 (EDT)
**2, [[User:Katherine Grace Johnson|Katherine Grace Johnson]] 14:51, 20 May 2015 (EDT)
**0, [[User:Natalie Williams|Natalie Williams]] 14:52, 20 May 2015 (EDT)
**0, [[User:Anindita Varshneya|Anindita Varshneya]] 14:54, 20 May 2015 (EDT)
**0, [[User:Kevin Patrick McGee|Kevin Patrick McGee]] 14:54, 20 May 2015 (EDT)

Revision as of 13:05, 20 May 2015

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SURP 2015 Schedule

Week Date Wet Lab GRNsight GRNmap Meetings & Events
1 Mon

May 18

AM: How to wiki, PowerPoint overview

PM: Within- and between-array normalization, one-strain ANOVA

Tues

May 19

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

  • 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
2 Tues

May 26

AM: F1 cDNA synthesis

PM: F1 cDNA purification, aRNA synthesis

Wed

May 27

  • Joint group meeting, 12:00-2:00 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

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
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

Strain Voting

Δino2

Δopi1

Δyap1

Δarg80

Δrsf2

Δrtg3

Δtbf1

Δyhp1

Δyox1

Δphd1

Δnrg1

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