Dahlquist:SURP 2015 Schedule: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(→‎SURP 2015 Schedule: added in note as to which students did which strains)
 
(12 intermediate revisions by 4 users not shown)
Line 21: Line 21:


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.
|  
|  
* All group members report to S120 for microarray data analysis
* All group members report to S120 for microarray data analysis
Line 43: Line 49:
| Work with GRNmap team
| 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
| Work with GRNmap team
Line 77: Line 83:
* 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:Journalclub_MHKW_20150527.pptx | Kevin and Monica's journal club Powerpoint; 05/27/2015]]
** [[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 2:00-3:00 PM, S202
* GRNmap meeting 2:00-4:00 PM, S202
|--
|--
|  
|  
Line 85: Line 91:


May 28
May 28
| MH/KW: repeat ''Δyap1'' F1 cDNA synthesis, ''Δyap1'' F1 cDNA purification, aRNA synthesis
| MH/KW: repeat ''Δyap1'' F1 cDNA synthesis, ''Δyap1'' F1 cDNA purification


KM: ''Δnrg1'' PCR gel, ''Δphd1'' genotyping PCR
KM: ''Δnrg1'' PCR gel, ''Δphd1'' genotyping PCR
Line 103: Line 109:


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
|
|
|  
|  
Line 114: Line 120:


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''
|
|
|  
|  
Line 125: Line 131:


June 3
June 3
| AM: F2 aRNA purification, quantification
|  
 
PM: F2 aRNA gel
|
|
|
|
|
|
* 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
|--
|--
| '''4'''
| '''4'''
Line 140: Line 147:


June 8
June 8
| AM: dry F2 aRNA, F3 cDNA synthesis
| KM: ''Δrsf2'', ''Δrtg3'' temp-sensitive growth expt on plates
 
PM: F2 label & hybe
|  
|  
|  
|  
Line 151: Line 156:


June 9
June 9
| AM: F2 wash & scan
|  
 
PM: F3 cDNa purification, aRNA synthesis
|  
|  
|  
|  
Line 161: Line 164:
| Wed
| Wed
June 10
June 10
| AM: F3 aRNA purification, quantification
|  
 
PM: F3 aRNA gel
|  
|  
|
|
|  
|  
* 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)]
** [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'''
Line 176: Line 179:


June 15
June 15
| AM: dry F3 aRNA, F4 cDNA synthesis
| KM: ''Δyhp1'', ''Δyox1'' temp-sensitive growth expt on plates
 
PM: F3 label & hybe
|  
|  
|
|
Line 187: Line 188:


June 16
June 16
| AM: F3 wash & scan
|  
 
PM: F4 cDNA purification, aRNA synthesis
|  
|  
|  
|  
Line 198: Line 197:


June 17
June 17
| AM: F4 aRNA purification, quantification
|  
 
PM: F4 aRNA gel
|  
|  
|
|
|  
|  
* 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
|--
|--
Line 212: Line 212:


June 22
June 22
| AM:
|  
 
PM: F4 label & hybe
|  
|  
|
|
Line 223: Line 221:


June 23
June 23
| AM: F4 wash & scan
|  
|  
|  
|
|
Line 240: Line 238:
|
|
* 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
|}
|}


Line 333: Line 336:


=== ''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)

Latest revision as of 14:37, 20 June 2016

Home        Research        Protocols        Notebook        People        Publications        Courses        Contact       


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

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Dahlquist:SURP_2015_Schedule&oldid=943447"