Team:Stanford/Notebook/Lab Work/Week 1

6/28 Monday

General Meeting Notes

• Wiki stuff
  • Everyone should sign up on 2010.igem.org website
    • Take advantage of the new calendar system
    • Need to transfer current website over
  • Current wiki needs a new vision
    • Francisco + Alex assembling wiki committee
• Transform the first wave of cells
  • Pick colonies
  • Colony PCR
  • Sequence parts to validate
    • Use the Smolke sequencing network
• Characterize promoters
  • Digest, ligate
  • Need to acquire enzymes
  • Need an PO account.
    • Email Jeanne
• Get competent cells
• Getting DNA
  • Assembly PCR
  • PCR from host cells
  • Synthesize de novo
• RNA team
  • Use RNAstructure
    • Maybe use ViennaRNA or dinamelt
  • Talk to Arkin and Berkeley Postdocs
  • Finalize sRNA library
  • 9kb plasmid
• Meeting scheudle
  • Monday morning is good for logistics
  • Group meetings for presentations
    • One person presents their work in the context of everything else
  • Journal club
  • Karina will set up a doodle

6/29 Tuesday

Laura's Notebook

• made LB agar (with Alex and Chris)
  • made 1 500 mL bottle, 3 250 mL bottles, then autoclaved

6/30 Wednesday

Laura's Notebook

• Re-try failed transformation (failed 2X for Alex and Chris)
• Protocol followed:

1. get competent cells from -80oC freezer
2. set H2O bath to 42oC (already done)
3. add 50 uL cells to a 1.5 mL tube (keep tubes on ice)
4. add 50 ng or 2.5 uL circular DNA to E. Coli (variation: used 5.0 uL I0500 this time)
5. on ice 30 min
6. 24oC H2O bath 20 sec.
7. on ice 15 min
8. add 1 mL SOC, 2 hours at 37oC (rotating)
9. plate100uL on appropriate plate (kanamycin this time), incubate 12-16 hours before picking colonies

• variations: 200 uL plated this time, also plated on kan/X-gal/IPTG plate (plasmid inducible copy # by X-gal)

7/1 Thursday

Laura's Notebook

• did 8 minipreps from Chris'/Alex's cultures
• used Qiagen spin kit, with the following variations:

1. skipped "recommended" wash step
2. eluted with H2O

• Concentrations from Nanodrop (taken by Chris B.)

• helped Karina, Francisco with the transformations of parts

Francisco's Notebook

• Learned how to transform using electroporation.

7/2 Friday

Recap Meeting Notes

• Things to think about:
  • name of the device (see if electronic analogue exists)
  • decouple the small RNA binding from the target gene ("RSID" tags)
  • leadership structure for the team