Dahlquist:SURP 2015 Schedule: Difference between revisions

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May 18
May 18
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| Work with GRNmap team
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| Work with GRNmap team
| AM: How to wiki, [https://lionshare.lmu.edu/Users/kdahlqui/SURP%202015/20150518_IntroSURP.ppt PowerPoint overview]
| AM: How to wiki, [https://lionshare.lmu.edu/Users/kdahlqui/SURP%202015/20150518_IntroSURP.ppt PowerPoint overview]


PM: [[Dahlquist:Microarray_Data_Analysis_Workflow | Within- and between-array normalization, one-strain ANOVA]]
PM: [[Dahlquist:Microarray_Data_Analysis_Workflow | 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.
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|  
* All group members report to S120 for microarray data analysis
* All group members report to S120 for microarray data analysis
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May 19
May 19
|  
| Work with GRNmap team
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| Work with GRNmap team
| AM: [[Dahlquist:Microarray_Data_Analysis_Workflow | Modified T test]]  
| AM: [[Dahlquist:Microarray_Data_Analysis_Workflow | Modified T test]]  


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May 20
May 20
|
| Work with GRNmap team
* Decide which strain to label and hybridize to microarrays: ''Δino2'', ''Δopi1'', or ''Δyap1''
* 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
* 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
| GenMAPP, YEASTRACT
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|  
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May 26  
May 26  
| AM: F1 cDNA synthesis
| Work with GRNmap team
| Work with GRNmap team; GRNsight code walk-through
| All: Create input sheet and run GRNmap


PM: F1 cDNA purification, aRNA synthesis
TM/TR: work on issue [https://github.com/kdahlquist/GRNmap/issues/74 #74]
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May 27
May 27
|  
| MH/KW: ''Δyap1'' F1 cDNA synthesis, ''Δyap1'' F1 cDNA purification, aRNA synthesis
 
KM: genotyping PCR ''Δnrg1''
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* GRNsight meeting 11:00-12:00 PM, S202
* Joint group meeting, 12:00-2:00 PM, S202
* Joint group meeting, 12:00-2:00 PM, S202
** Monica & Kevin W. present journal club
** Monica & Kevin W. present journal club
** [[Media:Journalclubpresentation.pptx | Kevin and Monica's journal club Powerpoint; 05/27/2015]]
** [http://aem.asm.org/content/80/14/4433.short Hebly et al. (2014)]
** [http://aem.asm.org/content/80/14/4433.short Hebly et al. (2014)]
* GRNmap meeting 2:00-4:00 PM, S202
|--
|--
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May 28
May 28
| AM: F1 aRNA purification, quantification
| MH/KW: repeat ''Δyap1'' F1 cDNA synthesis, ''Δyap1'' F1 cDNA purification


PM: F1 aRNA gel
KM: ''Δnrg1'' PCR gel, ''Δphd1'' genotyping PCR
|  
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| GJ/NW: work on issue [https://github.com/kdahlquist/GRNmap/issues/10 #10]
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* 1:00 PM, S120, Glenn Johnson-Grau: workshop on searching the literature  
* Glenn Johnson-Grau: workshop on searching the literature  
** [[Media:BIOL478_Spring2015_HW6_AnnotatedBibliography.pdf | BIOL478 Annotated Bibliography Assignment]]
*** [http://libguides.lmu.edu/BIOL478 BIOL478 LibGuide]
** [[BIOL368/F14:Week_3 | BIOL368 Annotated Bibliography Assignment]]
*** [http://libguides.lmu.edu/BIOL368 BIOL368 LibGuide]
*** [http://libguides.lmu.edu/BIOL367 BIOL367 LibGuide]
* Nicole's last day
* Nicole's last day
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June 1
June 1
| AM: dry F1 aRNA, F1 cDNA synthesis
| MH/KW: ''Δyap1'' F1 aRNA synthesis, purification, A260


PM: F1 label & hybe
KM: ''Δnrg1'', ''Δphd1'' temp-sensitive growth expt on plates
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June 2
June 2
| AM: F1 wash & scan
| MH/KW: ''Δyap1'' F1 aRNA gel, dry samples


PM: F2 cDNA purification, aRNA synthesis
KM: repeat ''Δphd1'' PCR w/wt template; PCR ''Δrsf2''
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June 3
June 3
| AM: F2 aRNA purification, quantification
|  
 
PM: F2 aRNA gel
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* GRNsight meeting 11:00-12:00 PM, S202
* Joint group meeting, 12:00-2:00 PM, S202
* Joint group meeting, 12:00-2:00 PM, S202
** Natalie & Kevin M. present journal club
** Natalie & Kevin M. present journal club
** [http://nar.oxfordjournals.org/content/41/18/8452.long Geistlinger et al. (2013)]
** [http://nar.oxfordjournals.org/content/41/18/8452.long Geistlinger et al. (2013)]
<!--** [http://genome.cshlp.org/content/19/4/556.short Zhu et al. (2009)]-->
<!--** [http://genome.cshlp.org/content/19/4/556.short Zhu et al. (2009)]-->
**[[Media:KM NW Journal Club CGRNds.pptx]]
* GRNmap meeting 2:00-4:00 PM, S202
|--
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| '''4'''
| '''4'''
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June 8
June 8
| AM: dry F2 aRNA, F3 cDNA synthesis
| KM: ''Δrsf2'', ''Δrtg3'' temp-sensitive growth expt on plates
 
PM: F2 label & hybe
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June 9
June 9
| AM: F2 wash & scan
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PM: F3 cDNa purification, aRNA synthesis
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| Wed
| Wed
June 10
June 10
| AM: F3 aRNA purification, quantification
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PM: F3 aRNA gel
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* GRNsight meeting 11:00-12:00 PM, S202
* Joint group meeting, 12:00-2:00 PM, S202
* Joint group meeting, 12:00-2:00 PM, S202
** (Grace), Tessa, & Trixie present journal club
** Grace, Tessa, & Trixie present journal club
** [http://nar.oxfordjournals.org/content/35/1/279.short Vu & Vohradsky (2007)]
** [http://nar.oxfordjournals.org/content/35/1/279.short Vu & Vohradsky (2007)]
** [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008121 Yip et al. (2010)]
* GRNmap meeting 2:00-4:00 PM, S202
|--
|--
| '''5'''
| '''5'''
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June 15
June 15
| AM: dry F3 aRNA, F4 cDNA synthesis
| KM: ''Δyhp1'', ''Δyox1'' temp-sensitive growth expt on plates
 
PM: F3 label & hybe
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June 16
June 16
| AM: F3 wash & scan
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PM: F4 cDNA purification, aRNA synthesis
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June 17
June 17
| AM: F4 aRNA purification, quantification
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PM: F4 aRNA gel
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* GRNsight meeting 11:00-12:00 PM, S202
* Joint group meeting, 12:00-2:00 PM, S202
* Joint group meeting, 12:00-2:00 PM, S202
** Brandon & (Grace) presents journal club
** [[Media:BK_Journal_Club_June17.pptx‎  | Brandon presents journal club]]
** [http://iovs.arvojournals.org/article.aspx?articleid=2127341 Chiu et al. (2012)]
* GRNmap meeting 2:00-4:00 PM, S202
* Natalie's last day
* Natalie's last day
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June 22
June 22
| AM:
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PM: F4 label & hybe
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June 23
June 23
| AM: F4 wash & scan
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* Joint group meeting, 12:00-2:00 PM, S202
* Joint group meeting, 12:00-2:00 PM, S202
** Everyone gives final research presentations
** [[Media:DahlquistLab_SURP_20150624.pptx| Group presentation for President Snyder]]
** Individual presentations
* 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]
** [https://github.com/kdahlquist/GRNmap/wiki/SURP-2015-Abstract-Grace-Johnson-and-Natalie-Williams Grace & Natalie's Abstract]
** [https://github.com/dondi/GRNsight/wiki/LMU-Undergraduate-Research-Symposium-2015-Abstract Anu's Abtract]
** [https://github.com/kdahlquist/GRNmap/wiki/SURP-2015-Abstract Tessa & Trixie's Abstract]
** Kevin M., Kevin W., and Monica's Abstract
|}
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=== ''Δtbf1''===
=== ''Δtbf1''===
* don't have
* don't have; essential gene, strain not available
*Within-strain
*Within-strain
** 0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:44, 20 May 2015 (EDT)
** 0, [[User:Tessa A. Morris|Tessa A. Morris]] 14:44, 20 May 2015 (EDT)
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=== ''Δarg80''===
=== ''Δarg80''===
* box 2-16 or 2-74
*Within-strain
*Within-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)

Latest revision as of 14:37, 20 June 2016

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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.
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
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

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
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

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
  • 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

6 Mon

June 22

Tues

June 23

Wed

June 24

Lab check-out

Lab check-out

Lab check-out

Strain Voting

Δyap1

Δino2

Δopi1

Δrtg3

Δrsf2

Δtbf1

Δyox1

Δyhp1

Δphd1

Δnrg1

Δarg80

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