Team:University of Chicago/Notebook

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Lab Calendar

Click to see what lab work was done each day!

Individual Lab Notebook Pages

Damon Wang's notebook
Parijata "Jata" notebook
Nora Yucel's notebook
Laura Stone's notebook
Rob McConeghy's notebook
Daniel M. Choi's notebook

If you did it, record it

Resources

[http://www.freewebs.com/genehackers/ Team Website (External Link)]

Recipes

Media

LB Broth (1 L)

1 L dH20
10 g Bacto tryptone
5 g Bacto yeast extract
5 g NaCl
1 mL 2N NaOH
12 g agar (optional)
- 3 g agar + 250 mL broth per bottle
Autoclave

Note: Add 3 mL 1 M CaCl2 before phage transductions

SOB Medium

Used in growing bacteria for preparing chemically competent cells

Ingredients

0.5% (w/v) yeast extract
2% (w/v) tryptone
10 mM NaCl
2.5 mM KCl
20 mM MgSO4

Per liter:

5 g yeast extract
20 g tryptone
0.584 g NaCl
0.186 g KCl
2.4 g MgSO4

Note: Some formulations of SOB use 10 mM MgCl2 and 10 mM MgSO4 instead of 20 mM MgSO4.

SOB medium is also available dry premixed from Difco, 0443-17.
Adjust to pH 7.5 prior to use. This requires approximately 25 ml of 1M NaOH per liter.

SOC Medium (per 100 ml)

Note This medium should be prepared immediately before use.

Add 2 ml of filter-sterilized 20% (w/v) glucose or 1 ml of filter-sterilized 2 M glucose to 100 ml sterile SOB

Buffers

CCMB80

10 mM KOAc pH 7.0 (10 ml of a 1M stock/L)
80 mM CaCl2.2H2O (11.8 g/L)
20 mM MnCl2.4H2O (4.0 g/L)
10 mM MgCl2.6H2O (2.0 g/L)
10% glycerol (100 ml/L)
adjust pH DOWN to 6.4 with 0.1N HCl if necessary
- adjusting pH up will precipitate manganese dioxide from Mn containing solutions.
sterile filter and store at 4°C
slight dark precipitate appears not to affect its function

5x Ligation Adjustment Buffer

Intended to be mixed with ligation reactions to adjust buffer composition to be near the CCMB80 buffer
KOAc 40 mM (40 ml/liter of 1 M KOAc soluProxy-Connection: keep-alive

Cache-Control: max-age=0

on, pH 7.0)

CaCl2 400 mM (200 ml/l of a 2 M solution)
MnCl2 100 mM (100 ml/l of a 1 M solution)
Glycerol 46.8% (468 ml/liter)
pH adjustment with 2.3% of a 10% acetic acid solution (12.8ml/liter)
- Previous protocol indicated amount of acetic acid added should be 23 ml/liter but that amount was found to be 2X too much per tests on 1.23.07 --Meaganl 15:50, 25 January 2007 (EST)
water to 1 liter
autoclave or sterile filter
Test pH adjustment by mixing 4 parts ligation buffer + 1 part 5x ligation adjustment buffer and checking pH to be 6.3 - 6.5
Reshma 10:49, 11 February 2008 (CST): Use of the ligation adjustment buffer is optional.

DNA and protein gels

Agar

0.8%

Weigh out .8g agarose
Put agarose in 500mL Erlenmeyer flask.
Add 100mL 1X TBE Buffer. Swirl.
Microwave at 100% power until the agarose starts to dissolve. Every 30-40 seconds, stop and swirl. Continue microwaving until solution boils and agarose is dissolved.
After agarose is dissolved, cover flask with foil or aran wrap and place in 55-60C waterbath until needed.
When Agarose has cooled to enough to touch comfortably, add 10microliters Syber Safe. Swirl.
Pour 30mL gels. Use 50Ml conical tube to measure 30mL.

1.2%

Same as above but use 1.2 g agarose instead of .8g

Protocols

Growing Cells

TOP10 Competent Cells

Prechill plasticware and glassware

Preparing seed stocks

Streak TOP10 cells on an SOB plate and grow for single colonies at 23°C
- room temperature works well
Pick single colonies into 2 ml of SOB medium and shake overnight at 23°C
- room temperature works well
Add glycerol to 15%
Aliquot 1 ml samples to Nunc cryotubes
Place tubes into a zip lock bag, immerse bag into a dry ice/ethanol bath for 5 minutes
- This step may not be necessary
Place in -80°C freezer indefinitely.

Preparing competent cells

Inoculate 250 ml of SOB medium with 1 ml vial of seed stock and grow at 20°C to an OD600nm of 0.3
- This takes approximately 16 hours.
- Controlling the temperature makes this a more reproducible process, but is not essential.
- Room temperature will work. You can adjust this temperature somewhat to fit your schedule
- Aim for lower, not higher OD if you can't hit this mark
Centrifuge at 3000g at 4°C for 10 minutes in a flat bottom centrifuge bottle.
- Flat bottom centrifuge tubes make the fragile cells much easier to resuspend
- It is often easier to resuspend pellets by mixing before adding large amounts of buffer
Gently resuspend in 80 ml of ice cold CCMB80 buffer
- sometimes this is less than completely gentle. It still works.
Incubate on ice 20 minutes
Centrifuge again at 4°C and resuspend in 10 ml of ice cold CCMB80 buffer.
Test OD of a mixture of 200 _l SOC and 50 _l of the resuspended cells.
Add chilled CCMB80 to yield a final OD of 1.0-1.5 in this test.
Incubate on ice for 20 minutes
Aliquot to chilled screw top 2 ml vials or 50 _l into chilled microtiter plates
Store at -80°C indefinitely.
- Flash freezing does not appear to be necessary
Test competence (see below)
Thawing and refreezing partially used cell aliquots dramatically reduces transformation efficiency by about 3x the first time, and about 6x total after several freeze/thaw cycles.

Measurement of competence

Transform 50 _l of cells with 1 _l of standard pUC19 plasmid (Invitrogen)
- This is at 10 pg/_l or 10-5 _g/_l
- This can be made by diluting 1 _l of NEB pUC19 plasmid (1 _g/_l, NEB part number N3401S) into 100 ml of TE
Hold on ice 0.5 hours
Heat shock 60 sec at 42C
Add 250 _l SOC
Incubate at 37 C for 1 hour in 2 ml centrifuge tubes rotated
- using 2ml centrifuge tubes for transformation and regrowth works well because the small volumes flow well when rotated, increasing aeration.
- For our plasmids (pSB1AC3, pSB1AT3) which are chloramphenicol and tetracycline resistant, we find growing for 2 hours yields many more colonies
- Ampicillin and kanamycin appear to do fine with 1 hour growth
Plate 20 _l on AMP plates using sterile 3.5 mm glass beads
- Good cells should yield around 100 - 400 colonies
- Transformation efficiency is (dilution factor=15) x colony count x 105/µgDNA
- We expect that the transformation efficiency should be between 5x108 and 5x109 cfu/µgDNA

Glycerol Stocks

Materials

40% glycerol solution
Cryogenic vials

Method

Add 1 ml of 40% glycerol in H2O to a cryogenic vial.
Add 1 ml sample from the culture of bacteria to be stored.
Gently vortex the cryogenic vial to ensure the culture and glycerol is well-mixed.
- Alternatively, pipet to mix.
Use a tough spot to put the name of the strain or some useful identifier on the top of the vial.
On the side of the vial list all relevant information - part, vector, strain, date, researcher, etc.
Store in a freezer box in a -80C freezer. Remember to record where the vial is stored for fast retrieval later.

Notes

While it is possible to make a long term stock from cells in stationary phase, ideally your culture should be in logarithmic growth phase. Prof. Schonbaum's version

Grow a 3 ml culture overnight
Add 200 µl 100% glycerol to 1 ml cells in a cryotube (final concentration should be 15-20% glycerol

    different concentrations from different protocols

Mix by vortexing and let sit for a little bit. Then put the tubes in the -80°C freezer.

@@ Line 77: / Line 77: @@
 ==== 5x Ligation Adjustment Buffer ====
 * Intended to be mixed with ligation reactions to adjust buffer composition to be near the CCMB80 buffer
-* KOAc 40 mM (40 ml/liter of 1 M KOAc solution, pH 7.0)
+* KOAc 40 mM (40 ml/liter of 1 M KOAc soluProxy-Connection: keep-alive
+Cache-Control: max-age=0
+on, pH 7.0)
 * CaCl2 400 mM (200 ml/l of a 2 M solution)
 * MnCl2 100 mM (100 ml/l of a 1 M solution)
@@ Line 108: / Line 111: @@
 ===== Preparing seed stocks =====
 # Streak TOP10 cells on an SOB plate and grow for single colonies at 23°C
-** room temperature works well
+#* room temperature works well
 # Pick single colonies into 2 ml of SOB medium and shake overnight at 23°C
-** room temperature works well
+#* room temperature works well
 # Add glycerol to 15%
 # Aliquot 1 ml samples to Nunc cryotubes
 # Place tubes into a zip lock bag, immerse bag into a dry ice/ethanol bath for 5 minutes
-** This step may not be necessary
+#* This step may not be necessary
 # Place in -80°C freezer indefinitely.
 ===== Preparing competent cells =====
-* Inoculate 250 ml of SOB medium with 1 ml vial of seed stock and grow at 20°C to an OD600nm of 0.3
+# Inoculate 250 ml of SOB medium with 1 ml vial of seed stock and grow at 20°C to an OD600nm of 0.3
-** This takes approximately 16 hours.
+#* This takes approximately 16 hours.
-** Controlling the temperature makes this a more reproducible process, but is not essential.
+#* Controlling the temperature makes this a more reproducible process, but is not essential.
-** Room temperature will work. You can adjust this temperature somewhat to fit your schedule
+#* Room temperature will work. You can adjust this temperature somewhat to fit your schedule
-** Aim for lower, not higher OD if you can't hit this mark
+#* Aim for lower, not higher OD if you can't hit this mark
-* Centrifuge at 3000g at 4°C for 10 minutes in a flat bottom centrifuge bottle.
+# Centrifuge at 3000g at 4°C for 10 minutes in a flat bottom centrifuge bottle.
-** Flat bottom centrifuge tubes make the fragile cells much easier to resuspend
+#* Flat bottom centrifuge tubes make the fragile cells much easier to resuspend
-** It is often easier to resuspend pellets by mixing before adding large amounts of buffer
+#* It is often easier to resuspend pellets by mixing before adding large amounts of buffer
-* Gently resuspend in 80 ml of ice cold CCMB80 buffer
+# Gently resuspend in 80 ml of ice cold CCMB80 buffer
-** sometimes this is less than completely gentle. It still works.
+#* sometimes this is less than completely gentle. It still works.
-* Incubate on ice 20 minutes
+# Incubate on ice 20 minutes
-* Centrifuge again at 4°C and resuspend in 10 ml of ice cold CCMB80 buffer.
+# Centrifuge again at 4°C and resuspend in 10 ml of ice cold CCMB80 buffer.
-* Test OD of a mixture of 200 _l SOC and 50 _l of the resuspended cells.
+# Test OD of a mixture of 200 _l SOC and 50 _l of the resuspended cells.
-* Add chilled CCMB80 to yield a final OD of 1.0-1.5 in this test.
+# Add chilled CCMB80 to yield a final OD of 1.0-1.5 in this test.
-* Incubate on ice for 20 minutes
+# Incubate on ice for 20 minutes
-* Aliquot to chilled screw top 2 ml vials or 50 _l into chilled microtiter plates
+# Aliquot to chilled screw top 2 ml vials or 50 _l into chilled microtiter plates
-* Store at -80°C indefinitely.
+# Store at -80°C indefinitely.
-** Flash freezing does not appear to be necessary
+#* Flash freezing does not appear to be necessary
-* Test competence (see below)
+# Test competence (see below)
-* Thawing and refreezing partially used cell aliquots dramatically reduces transformation efficiency by about 3x the first time, and about 6x total after several freeze/thaw cycles.
+# Thawing and refreezing partially used cell aliquots dramatically reduces transformation efficiency by about 3x the first time, and about 6x total after several freeze/thaw cycles.
 ===== Measurement of competence =====
-* Transform 50 _l of cells with 1 _l of standard pUC19 plasmid (Invitrogen)
+# Transform 50 _l of cells with 1 _l of standard pUC19 plasmid (Invitrogen)
-** This is at 10 pg/_l or 10-5 _g/_l
+#* This is at 10 pg/_l or 10-5 _g/_l
-** This can be made by diluting 1 _l of NEB pUC19 plasmid (1 _g/_l, NEB part number N3401S) into 100 ml of TE
+#* This can be made by diluting 1 _l of NEB pUC19 plasmid (1 _g/_l, NEB part number N3401S) into 100 ml of TE
-* Hold on ice 0.5 hours
+# Hold on ice 0.5 hours
-* Heat shock 60 sec at 42C
+# Heat shock 60 sec at 42C
-* Add 250 _l SOC
+# Add 250 _l SOC
-* Incubate at 37 C for 1 hour in 2 ml centrifuge tubes rotated
+# Incubate at 37 C for 1 hour in 2 ml centrifuge tubes rotated
-** using 2ml centrifuge tubes for transformation and regrowth works well because the small volumes flow well when rotated, increasing aeration.
+#* using 2ml centrifuge tubes for transformation and regrowth works well because the small volumes flow well when rotated, increasing aeration.
-** For our plasmids (pSB1AC3, pSB1AT3) which are chloramphenicol and tetracycline resistant, we find growing for 2 hours yields many more colonies
+#* For our plasmids (pSB1AC3, pSB1AT3) which are chloramphenicol and tetracycline resistant, we find growing for 2 hours yields many more colonies
-** Ampicillin and kanamycin appear to do fine with 1 hour growth
+#* Ampicillin and kanamycin appear to do fine with 1 hour growth
-* Plate 20 _l on AMP plates using sterile 3.5 mm glass beads
+# Plate 20 _l on AMP plates using sterile 3.5 mm glass beads
-** Good cells should yield around 100 - 400 colonies
+#* Good cells should yield around 100 - 400 colonies
-** Transformation efficiency is (dilution factor=15) x colony count x 105/µgDNA
+#* Transformation efficiency is (dilution factor=15) x colony count x 105/µgDNA
-** We expect that the transformation efficiency should be between 5x108 and 5x109 cfu/µgDNA
+#* We expect that the transformation efficiency should be between 5x108 and 5x109 cfu/µgDNA
 ===== Glycerol Stocks =====
@@ Line 162: / Line 165: @@
 ====== Method ======
-* Add 1 ml of 40% glycerol in H2O to a cryogenic vial.
+# Add 1 ml of 40% glycerol in H2O to a cryogenic vial.
-* Add 1 ml sample from the culture of bacteria to be stored.
+# Add 1 ml sample from the culture of bacteria to be stored.
-* Gently vortex the cryogenic vial to ensure the culture and glycerol is well-mixed.
+# Gently vortex the cryogenic vial to ensure the culture and glycerol is well-mixed.
-** Alternatively, pipet to mix.
+#* Alternatively, pipet to mix.
-* Use a tough spot to put the name of the strain or some useful identifier on the top of the vial.
+# Use a tough spot to put the name of the strain or some useful identifier on the top of the vial.
-* On the side of the vial list all relevant information - part, vector, strain, date, researcher, etc.
+# On the side of the vial list all relevant information - part, vector, strain, date, researcher, etc.
-* Store in a freezer box in a -80C freezer. Remember to record where the vial is stored for fast retrieval later.
+# Store in a freezer box in a -80C freezer. Remember to record where the vial is stored for fast retrieval later.
 ====== Notes ======