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Team:Calgary/Notebook/Calendar/ChipSEQ
From 2011.igem.org
Notebook
Post-Regionals
Journal
- Defining Objectives
- Techniques Workshop
- Bioinformatics & qRT-PCR
- Sensory Element Fishing
- Electrochem - CPR Oxidation
- Electrochem - Reporter Gene
- Pseudomonas Tools
- Microalgae Tools
- NA Viability Assays
- May - July Group Journal
Protocols
Safety
Sensory Element Fishing Project
Project Participants
Robert
July 8-14, 2011
Author: Robert
Friday, July 8, 2011
Running assay to determine the viability of pseudomonas #29 and #30 in NA as well as to see if it can degrade NA. Counting colonies on plates to see how many cells are alive and checking OD readings to see the number of cells alive and dead present in the sample. Also made overnight culture of strains LD1 and LD2.
Saturday, July 9, 2011
Running assay still. Counting colonies on plates and checking OD readings, same as before. Used the overnight cultures made on friday to make glycerol stocks of LD1 and LD2.
Sunday, July 10, 2011
Running assay still. Counting colonies on plates and checking OD readings, same as before.
Monday, July 11, 2011
Finished assay with last readings. OD was not helpful but the plate readings gave interesting data. Streaked the bacteria on McConkey media to check for contamination. Planned next assay.
Tuesday, July 12, 2011
Re-streaked bacteria on McConkey media, as the first round gave confusing results. Started a growth curve of pseudomonas LD1 and LD2 in NA to determine wether or not they can grow in the presence of NA in a rich LB media and if so, how fast.
Wednesday, July 13, 2011
Finished growth curve, the LD strains grow better than the #29 and #30 strains. Prepared media for next assay with the Del-Rio strains. Made overnight cultures for the assay.
Thursday, July 14, 2011
Started assay with LD1 and LD2 at 22,26, and 37*C in both Focht minial media and LB broth to see at what conditions they grow best at and to see if combined cultures do better than individual strains. Started preparing for the ChIP-Seq experiment by finishing the buffers that Dave started the day before. Performed optimization experiment on shearing genomic DNA through sonication (lyse cells, shear DNA, run DNA on a gel to determine size). Gel picture below.
July 23-28, 2011
Author: Emily
Many more attempts at sonication were also performed on pseudomonas, as well as on E. Coli, which we had expected to work quite well. No success was achieved, so attempts were done where we varied the amplitude as well as the number of sonication cycles. De-cross linking after sonication was also attempted as well as digesting pseudomonas lysate with Sau3A. Finally, putative pseudomonas plasmids were treated with RNAse A and used as template in a verification PCR, however there are still no results for this.
