Sam:LabNotes/Microbiome-new/2011-3-31: Difference between revisions

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='''Single E.coli cell isolation using micromanipulation'''
='''Single E.coli cell isolation using micromanipulation'''=


==Background==
==Background==
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**Add 2uL E.colu culture(10^9 CFU/mL) with 200uL 10X dye (SYBR / DAPI). Incubate at 37C on the shaker for >30min.
**Add 2uL E.colu culture(10^9 CFU/mL) with 200uL 10X dye (SYBR / DAPI). Incubate at 37C on the shaker for >30min.
**Dilute the stained cell from 10^7 CFU/mL to 10^5 CFU/mL with 1X PBS.
**Dilute the stained cell from 10^7 CFU/mL to 10^5 CFU/mL with 1X PBS.
==E.coli cell micromanipulation test==
*Test of non-stained cell at BF, 10X condition
**Able to target (see) cells with a drop (8~10uL) of 10^4 CFU/mL ~ 10^5 CFU/mL diluted E.coli cells
**10^5 CFU/mL is still a little bit too dense for targeting a single cells. 10^4 CFU/mL is probably the best density.
*Challenges:
**E.coli cell is floating around and difficult to locate
**Contaminaiton of debris (some of them have size larger than an E.coli cell)
**Not able to tell if the target is E.coli or dust or debris.
**Fluorescent stained E.coli need to observed
*Lessons learned:

Revision as of 07:14, 2 April 2011

Single E.coli cell isolation using micromanipulation

Background

  • Collabrate with Andy Chen
  • Adapt the successful experience of micromanipulation on single human lymphocyte

Fresh E.coli cells recovery

  • Recovery fresh E.coli K-12 cell from glycerol stock (-80C)
    • Prepare 10mL pre-warmed LB in 10mL culture tube (x4)
    • Innoculate E.coli K-12 into the LB mediua(using 10p tips)
    • Cap the tube. Vortexing briefly. Incubate at 37C over night (3:00PM~9:00AM next day)
    • (The medium look cloudy in all of four tubes)
  • Washing cells
    • Pellet the cell by centrifuging.
    • Centrifuge the 10mL culture tubes at 3000rpm, 4C, 10min. Discard supernatant.
    • Resuspend the pellet in 1.5mL 1X PBS. Transfer into a 1.7mL tube.
    • Centrifuge the tube at 8000g, RT, 3min. Discard supernatant.
    • Resuspend the pellet in 1.0mL 1X PBS.
    • Repeat the last washing step again (Two times PBS washing in total).
    • Based on the culture cloudy extent, I estimate it's about 10^9 CFU/mL

E.coli stain (SYBR-green / DAPI)

  • Prepare dilued staining dye
    • Dilute SYBR(200X) into 10X by 1/20 dilution in a 1.7mL tube wrapped in foil
    • Thaw DAPI(10,000X)stock solution. Dilute DAPI into 10X by 1/1000 dilution in a 1.7mL tube wrapped in foil.
  • Cell staining
    • Add 2uL E.colu culture(10^9 CFU/mL) with 200uL 10X dye (SYBR / DAPI). Incubate at 37C on the shaker for >30min.
    • Dilute the stained cell from 10^7 CFU/mL to 10^5 CFU/mL with 1X PBS.

E.coli cell micromanipulation test

  • Test of non-stained cell at BF, 10X condition
    • Able to target (see) cells with a drop (8~10uL) of 10^4 CFU/mL ~ 10^5 CFU/mL diluted E.coli cells
    • 10^5 CFU/mL is still a little bit too dense for targeting a single cells. 10^4 CFU/mL is probably the best density.
  • Challenges:
    • E.coli cell is floating around and difficult to locate
    • Contaminaiton of debris (some of them have size larger than an E.coli cell)
    • Not able to tell if the target is E.coli or dust or debris.
    • Fluorescent stained E.coli need to observed
  • Lessons learned: