May
Week 1
- 05/09/2023 - Make common stocks needed for wet lab experiments & dipsticks
- 05/11/2023 - Test primers and PCR for activity
- 05/12/2023 - Ran gels on primer activity and PCR
Making Dipsticks
Week 2
- 05/15/2023 - Test gel electrophoresis ladder resolution
- 05/16/2023 - Test dipstick on E. coli and run PCR on gapA gene
- 05/18/2023 - Run first LAMP reaction and test/dilute our primers
- 05/19/2023 - Gel electrophoresis and analysis of first LAMP reaction
Week 4
- 05/30/2023 - Identify our best set of primers under various conditions
June
Week 2
- 06/21/2023 - Try new SYBR Safe to resolve resolution problems with gel electrophoresis
- 06/22/2023 - PCR on gapA gene
- 06/23/2023 - Run gel electrophoresis on LAMP reactions with human cells
Preparing to run LAMP reaction
July
Week 1
- 07/06/2023 - Begin work on qPCR to obtain differential fluorescence between our two DNA fragment samples
Week 2
- 07/11/2023 - More LAMP on our DNA fragments with qPCR fluorescence readings
- 07/12/2023 - Fluorescent testing of standard probe concentrations on LAMP product
- 07/13/2023 - Testing how the concentration of probes will affect our fluorescence results
- 07/14/2023 - LAMP on cultured human cells
Week 3
- 07/17/2023 - Testing dipstick method on human cells
- 07/18/2023 - Test how serial dilutions of amplified DNA affect fluorescence
- 07/19/2023 - DNA cleanup and lysis on LAMP products
- 07/20/2023 - Test how LAMP amplification is affected by the concentration of MgSO4 in reaction
Week 4
- 07/27/2023 - Testing HEK cells with and without our SNP on qPCR
- 07/28/2023 - Testing water bath method for LAMP optimization
Pipetting samples into a gel
August
Week 1
- 07/31/2023 - Testing cell dilutions and seeing if our negative control is contaminated
- 08/01/2023 - Probe optimization
- 08/02/2023 - Probe testing with increaced replicates to test technical variation
- 08/04/2023 - Primer optimization
Week 2
- 08/08/2023 - dNTP optimization and testing for negative control contamination
- 08/11/2023 - Testing fluorescence with 5x more quencher
Week 4
- 08/29/2023 - Restriction enzyme test on AleI
- 08/30/2023 - Gel electrophoresis on restriction enzyme test
Pouring gel to run electrophoresis
September
Week 1
- 09/05/2023 - Diagnostic digest
- 09/07/2023 - Run qPCR on sink titration experiment
- 09/07/2023 - PCR of oligos using 5 LAMP primer sets
- 09/08/2023 - Rerun restriction digest test to validate product identity
Week 2
- 09/12/2023 - Run asymmetric PCR
- 09/13/2023 - Run probes on asymmetric PCR, clean up LAMP product, run overnight digest on LAMP product
- 09/14/2023 - Run probes on asymmetric PCR, clean up LAMP product, run overnight digest on LAMP product
Week 3
- 09/18/2023 - Replication of LAMP reaction from Hyman paper again
- 09/19/2023 - Asymmetric PCR of our templates
- 09/20/2023 - Clean up the LAMP product and submit for sequencing
Week 4
Preparing qPCR plate for probes testing