Difference between revisions of "20.109(S19):Class data"
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==Module 2: Measuring gene expression== | ==Module 2: Measuring gene expression== | ||
+ | |||
+ | Heatmap with ALL genes for DLD-1 & BRCA2-/-: [[Media:Heatmap 19773 genes.pdf| linked here]] | ||
===M2D9=== | ===M2D9=== | ||
+ | |||
====qPCR results==== | ====qPCR results==== | ||
+ | {| border=1px | ||
+ | |'''Team''' | ||
+ | |'''qPCR Results''' | ||
+ | |- | ||
+ | |colspan=3|'''T/R''' | ||
+ | |- | ||
+ | |Red | ||
+ | |[[Media:Sp19_qPCR_TRred.xlsx|Sp19_qPCR_TRred]] | ||
+ | |- | ||
+ | |Orange | ||
+ | |[[Media:Sp19_qPCR_TRorange.xlsx|Sp19_qPCR_TRorange]] | ||
+ | |- | ||
+ | |Yellow | ||
+ | |[[Media:Sp19_qPCR_TRyellow.xlsx|Sp19_qPCR_TRyellow]] | ||
+ | |- | ||
+ | |Green | ||
+ | |[[Media:Sp19_qPCR_TRgreen.xlsx|Sp19_qPCR_TRgreen]] | ||
+ | |- | ||
+ | |Blue | ||
+ | |[[Media:Sp19_qPCR_TRblue.xlsx|Sp19_qPCR_TRblue]] | ||
+ | |- | ||
+ | |Pink | ||
+ | |[[Media:Sp19_qPCR_TRpink.xlsx|Sp19_qPCR_TRpink]] | ||
+ | |- | ||
+ | |Purple | ||
+ | |[[Media:Sp19_qPCR_TRpurple.xlsx|Sp19_qPCR_TRpurple]] | ||
+ | |- | ||
+ | |White | ||
+ | |[[Media:Sp19_qPCR_TRwhite.xlsx|Sp19_qPCR_TRwhite]] | ||
+ | |- | ||
+ | |Platinum | ||
+ | |[[Media:Sp19_qPCR_TRplat.xlsx|Sp19_qPCR_TRplatinum]] | ||
+ | |- | ||
+ | |colspan=3|'''W/F''' | ||
+ | |- | ||
+ | |Red | ||
+ | |[[Media:Sp19_WFred_qPCR.xlsx|Sp19_WFred_qPCR]] | ||
+ | |- | ||
+ | |Orange | ||
+ | |[[Media:Sp19_WForange_qPCR.xlsx|Sp19_WForange_qPCR]] | ||
+ | |- | ||
+ | |Yellow | ||
+ | |[[Media:Sp19_WFyellow_qPCR.xlsx|Sp19_WFyellow_qPCR]] | ||
+ | |- | ||
+ | |Green | ||
+ | |[[Media:Sp19_WFgreen_qPCR.xlsx|Sp19_WFgreen_qPCR]] | ||
+ | |- | ||
+ | |Blue | ||
+ | |[[Media:Sp19_WFblue_qPCR.xlsx|Sp19_WFblue_qPCR]] | ||
+ | |- | ||
+ | |Pink | ||
+ | |[[Media:Sp19_WFpink_qPCR.xlsx|Sp19_WFpink_qPCR]] | ||
+ | |- | ||
+ | |Gray | ||
+ | |[[Media:Sp19_WFgrey_qPCR.xlsx|Sp19_WFgrey_qPCR]] | ||
+ | |- | ||
+ | |} | ||
+ | <br> | ||
+ | {| border=1px | ||
====CellTiter Glo results==== | ====CellTiter Glo results==== | ||
+ | |||
+ | WF CTG raw data (plates)<br> | ||
+ | Plate 1: Pink / Grey Teams ([[Media:WF CellTIterGlo Plate1.xls| linked here]])<br> | ||
+ | Plate 2: Blue / Green / Yellow Teams ([[Media:WF CellTiterGlo Plate2.xls| linked here]])<br> | ||
+ | Plate 3: Red / Orange Teams ([[Media:WF CellTiterGlo Plate3.xls| linked here]])<br> | ||
{| border=1px | {| border=1px | ||
Line 301: | Line 368: | ||
|- | |- | ||
|Red | |Red | ||
− | | | + | |[[Media:Red_TR_CTGResults.xlsx]] |
+ | |[[Media:Sp19_CTGimages_red.zip]] | ||
|- | |- | ||
|Orange | |Orange | ||
− | | | + | |[[Media:Sp19_CTG_orange.xlsx]] |
+ | |[[Media:Sp19_CTGimages_orange.zip]] | ||
|- | |- | ||
|Yellow | |Yellow | ||
− | | | + | |[[Media:Sp19_CTG_yellow.xlsx]] |
+ | |[[Media:Sp19_CTGimages_yellow.zip]] | ||
|- | |- | ||
|Green | |Green | ||
− | | | + | |[[Media:Sp19_CTG_green.xlsx]] |
+ | |[[Media:Sp19_CTGimages_green.zip]] | ||
|- | |- | ||
|Blue | |Blue | ||
− | | | + | |[[Media:Sp19_CTG_blue.xlsx]] |
+ | |[[Media:Sp19_CTGimages_blue.zip]] | ||
|- | |- | ||
|Pink | |Pink | ||
− | | | + | |[[Media:Sp19_CTG_pink.xlsx]] |
+ | |[[Media:Sp19_CTGimages_pink.zip]] | ||
|- | |- | ||
|Purple | |Purple | ||
− | | | + | | [[Media: Sp19_TR_Purple_CellViability.xlsx]] |
+ | |[[Media:Sp19_CTGimages_Purple.zip]] | ||
|- | |- | ||
|White | |White | ||
− | | | + | | [[Media:Sp19_CTG_white.xlsx]] |
+ | [[Media:Sp19_CTG_white_analysis.xlsx]] | ||
+ | |[[Media:Sp19_CTGimages_white.zip]] | ||
|- | |- | ||
|Platinum | |Platinum | ||
− | | | + | | [[Media:Sp19_CTG_platinum.xlsx]] |
+ | | | ||
|- | |- | ||
|colspan=3|'''W/F''' | |colspan=3|'''W/F''' | ||
|- | |- | ||
|Red | |Red | ||
− | | | + | | [[Media: Sp19 20109 CTG WedWF.xlsx]] |
|- | |- | ||
|Orange | |Orange | ||
− | | | + | |[[Media:S19 WF Orange CellViability.xlsx]] |
|- | |- | ||
|Yellow | |Yellow | ||
− | | | + | |[[Media:WF_Yellow_CellTiterGlo.xlsx]] |
|- | |- | ||
|Green | |Green | ||
− | | | + | |[[Media:Sp19_20109_CTG_template_WF_Green.xlsx]] |
|- | |- | ||
|Blue | |Blue | ||
− | | | + | |[[Media:CTG_blue_team_wf.xlsx]] |
|- | |- | ||
|Pink | |Pink | ||
− | | | + | |[[Media:WF_Pink_cellviability.xlsx]] |
|- | |- | ||
|Grey | |Grey | ||
− | | | + | |[[Media:Sp19_20109_CTG_GREYWF.xlsx]] |
|- | |- | ||
|} | |} | ||
<br> | <br> | ||
− | |||
==Module 3: Engineering biomaterials== | ==Module 3: Engineering biomaterials== | ||
+ | |||
+ | ===WF phage-AuNP images=== | ||
+ | Red Team: [[Media:Sp19 WFRed phage-AuNP.jpg | linked here]] <br> | ||
+ | Orange Team: [[Media:Sp19 WFOrange phage-AuNP.jpg | linked here]]<br> | ||
+ | Yellow Team: [[Media:Sp19 WFYellow phage-AuNP.jpg | linked here]]<br> | ||
+ | Green Team: [[Media:Sp19 WFGreen phage_AuNP.jpg | linked here]]<br> | ||
+ | Blue Team: [[Media:Sp19 WFBlue phage-AuNP.jpg | linked here]]<br> | ||
+ | Pink Team: [[Media:Sp19 WFPink phage-AuNP.jpg | linked here]]<br> | ||
+ | Grey Team: [[Media:Sp19 WFGrey phage-AuNP.jpg | linked here]]<br> | ||
+ | |||
+ | ===Battery Capacity Raw Data=== | ||
+ | [[Media: M3_Battery_capacity_data_spring2019.xlsx|Battery Capacity Raw Data]]<br> | ||
+ | |||
+ | ===No-gold battery data=== | ||
+ | [[Media: Sp19_No_Gold_Control.zip |No gold control TEM and EDX images]]<br> | ||
+ | |||
+ | {| border=1px | ||
+ | |'''Experimental battery composition (AuNP/phage)''' | ||
+ | |'''Weight of cathode (mg)''' | ||
+ | |'''Actual capacity (mA*h/g)''' | ||
+ | |- | ||
+ | | 0 | ||
+ | | 3.17 | ||
+ | | 134.82 | ||
+ | |} | ||
+ | |||
+ | ===TR Battery information=== | ||
+ | {| border=1px | ||
+ | |'''Team''' | ||
+ | |'''Experimental battery composition (AuNP/phage)''' | ||
+ | |'''Weight of cathode (mg)''' | ||
+ | |'''Actual capacity (mA*h/g)''' | ||
+ | |- | ||
+ | |Red | ||
+ | |25 | ||
+ | |2.95 | ||
+ | |135.5932 | ||
+ | |- | ||
+ | |Orange | ||
+ | | 10 | ||
+ | | 2.77 | ||
+ | | 113.18 | ||
+ | |- | ||
+ | |Yellow | ||
+ | |20 | ||
+ | | 2.26 | ||
+ | |130.12 | ||
+ | |- | ||
+ | |Green | ||
+ | | 25 | ||
+ | | 2.83 | ||
+ | | 113.271 | ||
+ | |- | ||
+ | |Blue | ||
+ | | 20 | ||
+ | | 1.98 | ||
+ | | 103.63 | ||
+ | |- | ||
+ | |Pink | ||
+ | | 10 | ||
+ | | 2.06 | ||
+ | | 128.19 | ||
+ | |- | ||
+ | |Purple | ||
+ | | 33 | ||
+ | | 3.46 | ||
+ | | 106.40 | ||
+ | |- | ||
+ | |White | ||
+ | | 31 | ||
+ | |2.89 | ||
+ | | 89.313 | ||
+ | |- | ||
+ | |Platinum | ||
+ | | 30 | ||
+ | | 2.02 | ||
+ | | 98.6432 | ||
+ | |} | ||
+ | |||
+ | ===WF Battery information=== | ||
+ | {| border=1px | ||
+ | |'''Team''' | ||
+ | |'''Experimental battery composition (AuNP/phage)''' | ||
+ | |'''Weight of cathode (mg)''' | ||
+ | |'''Actual capacity (mA*h/g)''' | ||
+ | |- | ||
+ | |Red | ||
+ | | 35 | ||
+ | | 3.4 | ||
+ | | 43.519 | ||
+ | |- | ||
+ | |Orange | ||
+ | | 25 | ||
+ | | 1.29 | ||
+ | | 119.8 | ||
+ | |- | ||
+ | |Yellow | ||
+ | | 40 | ||
+ | | 1.70 | ||
+ | | 133.55 | ||
+ | |- | ||
+ | |Green | ||
+ | | 25 | ||
+ | | 2.52 | ||
+ | | 109.6413874 | ||
+ | |- | ||
+ | |Blue | ||
+ | | 30 | ||
+ | | 1.87 | ||
+ | | 88.43335 | ||
+ | |- | ||
+ | |Pink | ||
+ | | 20 | ||
+ | | 1.71 | ||
+ | | 71.5833 | ||
+ | |- | ||
+ | |Grey | ||
+ | | 14 | ||
+ | | 3.33 | ||
+ | | 99.2103 | ||
+ | |} |
Latest revision as of 20:04, 8 May 2019
Contents
Module 1: Assessing ligand binding
M1D3: SMM analysis
Files for SMM analysis
GAL files linked here.
Scan images and set numbers assigned to each team:
Team | Slide #1 | Slide #2 |
T/R | ||
Red | 14399983, set 1 | 14400077, set 4 |
Orange | 14400113, set 2 | 14400139, set 3 |
Yellow | 14400114, set 2 | 14400140, set 3 |
Green | 14399984, set 5 | 14399988, set 6 |
Blue | 14400072, set 5 | 14399987, set 6 |
Pink | 14399983, set 1 | 14400128, set 7 |
Purple | 14400077, set 4 | 14399959, set 8 |
White | 14400129, set 7 | 14400081, set 9 |
Grey | 14400128, set 7 | 14399959, set 8 |
W/F | ||
Red | 14400129, set 7 | 14400081, set 9 |
Orange | 14400128, set 7 | 14399959, set 8 |
Yellow | 14400143, set 11 | 14399950, set 12 |
Green | 14400147, set 10 | 14399951, set 12 |
Blue | 14400146, set 10 | 14399947, set 11 |
Pink | 14399983, set 1 | 14400077, set 4 |
Grey | 14400113, set 2 | 14400139, set 3 |
In spring 2017 Rob Wilson manually confirmed the top-ranking ~1000 compounds of the class's SMM screen. 72 can be recognized as hits with high confidence, and in total, 134 would be worth a hypothetical secondary screen. This corresponds to hit rate of about 0.15%, low and reasonable in the Koehler Lab's viewpoint. The conserved structures Rob identified are: a 7-azaindole and a 3,4 cis pyrrolidine with a nearby tertiary amine non-aromatic heterocycle.
Ligand selections
Team | Ligand #1 (short #) | Ligand #2 (short #) |
T/R | ||
Red | 31064975 (15) | 13742946 (16) |
Orange | 83759472 (2) | 34120495 (13) |
Yellow | 83759472 (2) | 64183606 (5) |
Green | 85836506 (1) | 41507070 (11) |
Blue | 71743840 (14) | 64472564 (4) |
Pink | 47464042 (8) | 85836506 (1) |
Purple | 47464042 (8) | 63365116 (6) |
White | 62716075 (7) | 45527639 (10) |
Grey | 62716075 (7) | 64472564 (4) |
W/F | ||
Red | 41507070 (11) | 13742946 (16) |
Orange | 34297777 (12) | 64183606 (5) |
Yellow | 45714400 (9) | 31064975 (15) |
Green | 34120495 (13) | 71743840 (14) |
Blue | 65421147 (3) | 45527639 (10) |
Pink | 63365116 (6) | 45714400 (9) |
Grey | 41507070 (11) | 65421147 (3) |
M1D3: Evaluate protein purity and concentration
WF Section
BCA Assay results (A562 measurements): linked here
SDS-PAGE images:
Red Team
Orange Team
Yellow Team
Green Team
Blue Team
Pink Team
Grey Team
M1D5: PPIase assay
TR Section
Plate #1: linked here
Plate #2: linked here
WF Section
Plate #1: linked here
Plate #2: linked here
Plate #3: linked here
M1D6: DSF results
TR Section
First Derivative: linked here
Melt Curve: linked here
WF Section
First Derivative: linked here
Melt Curve: linked here
M1D7: Data analysis
Team | PPIase results | DSF results |
T/R | ||
Red | DSF red | PPiase red |
Orange | DSF orange | PPiase orange |
Yellow | DSF yellow | PPiase yellow |
Green | DSF green | PPiase green |
Blue | DSF blue | PPiase blue |
Pink | DSF pink | PPiase pink |
Purple | DSF purple | PPiase purple |
White | DSF white | PPiase white |
Platinum | DSF platinum | PPiase platinum |
W/F | ||
Red | PPIase Red | DSF Red |
Orange | PPIase Orange | DSF Orange |
Yellow | PPiase Yellow | DSF Yellow |
Green | PPIase Green | DSF Green |
Blue | PPIase Blue | DSF Blue |
Pink | PPIase Pink | DSF Pink |
Grey | PPIase Grey | DSF Grey |
Module 2: Measuring gene expression
Heatmap with ALL genes for DLD-1 & BRCA2-/-: linked here
M2D9
qPCR results
Team | qPCR Results | |
T/R | ||
Red | Sp19_qPCR_TRred | |
Orange | Sp19_qPCR_TRorange | |
Yellow | Sp19_qPCR_TRyellow | |
Green | Sp19_qPCR_TRgreen | |
Blue | Sp19_qPCR_TRblue | |
Pink | Sp19_qPCR_TRpink | |
Purple | Sp19_qPCR_TRpurple | |
White | Sp19_qPCR_TRwhite | |
Platinum | Sp19_qPCR_TRplatinum | |
W/F | ||
Red | Sp19_WFred_qPCR | |
Orange | Sp19_WForange_qPCR | |
Yellow | Sp19_WFyellow_qPCR | |
Green | Sp19_WFgreen_qPCR | |
Blue | Sp19_WFblue_qPCR | |
Pink | Sp19_WFpink_qPCR | |
Gray | Sp19_WFgrey_qPCR |
Experimental battery composition (AuNP/phage) | Weight of cathode (mg) | Actual capacity (mA*h/g) |
0 | 3.17 | 134.82 |
TR Battery information
Team | Experimental battery composition (AuNP/phage) | Weight of cathode (mg) | Actual capacity (mA*h/g) |
Red | 25 | 2.95 | 135.5932 |
Orange | 10 | 2.77 | 113.18 |
Yellow | 20 | 2.26 | 130.12 |
Green | 25 | 2.83 | 113.271 |
Blue | 20 | 1.98 | 103.63 |
Pink | 10 | 2.06 | 128.19 |
Purple | 33 | 3.46 | 106.40 |
White | 31 | 2.89 | 89.313 |
Platinum | 30 | 2.02 | 98.6432 |
WF Battery information
Team | Experimental battery composition (AuNP/phage) | Weight of cathode (mg) | Actual capacity (mA*h/g) |
Red | 35 | 3.4 | 43.519 |
Orange | 25 | 1.29 | 119.8 |
Yellow | 40 | 1.70 | 133.55 |
Green | 25 | 2.52 | 109.6413874 |
Blue | 30 | 1.87 | 88.43335 |
Pink | 20 | 1.71 | 71.5833 |
Grey | 14 | 3.33 | 99.2103 |