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Buffer Preparation


This page is meant to serve as a centralized repository for all buffers and solutions used by the Pugh Lab as well as guide new members on preparation procedures.


General Notes


Making Solutions

Use 50% of the total volume to dissolve the solid or liquid components of the buffers unless the protocol states otherwise. Pour the solution into a graduated cylinder once the components are dissolved and bring up to the final volume with ddH2O. Filter sterilize with a Nalgene® Rapid-Flow™ Filter Unit of the appropriate size, and store at the recommended temperature listed under each recipe.

pH/Conductivity Readings

pH Probe Checklist

pH Probe Diagram

Before using the pH probe, ensure that the following list of requirements are met:

  • pH probe is full to the middle of the crosshairs with filling solution.
  • pH probe is rinsed with ddH2O and DABBED with a Kimwipe after rinsing.
  • Parafilm and blue plug removed from the neck of the probe-->replace when finished.
  • pH probe has been calibrated in last 30 days.
  • All measurements taken from consistent depth in the solution (at least beyond dark red/orange part of probe).

Conductivity Probe Checklist

Conductivity Probe Diagram

Before using the conductivity probe, ensure that the following list of requirements are met:

  • Probe is rinsed with ddH20 and DABBED with a Kimwipe after rinsing.
  • Probe has been calibrated in last 30 days.
  • All measurements are taken from consistent depth in the solution (at least beyond opening at bottom of the probe).

Buffer Recipes


Reagents and Stock Solutions

10X PBS (1 L)

Final Conc. of ComponentMW (g/mol)Amount
27 mM KCl74.552 g
14.7 mM KH2PO4 (monobasic)136.092 g
1.379 M NaCl58.4480 g
81 mM Na2HPO4 (dibasic)141.9611.5 g

Bring final volume to 1 L with ddH2O in a graduated cylinder. Filter sterilize and store at RT.

 

10mM Tris-HCl, pH 7.5 (2 L)

Final Conc. of ComponentStockAmount
10 mM Tris-HCl, pH 7.51 M20 mL

Bring final volume to 2 L with ddH2O in a graduated cylinder. Filter sterilize and store at RT.

 

TE (Tris-EDTA) (500 mL)

Final Conc. of ComponentStockAmount
10 mM Tris-HCl, pH 8.01 M5 mL
1 mM EDTA, pH 8.00.5 M1 mL

Bring final volume to 500 mL with ddH2O in a graduated cylinder. Filter sterilize and store at RT.

 

2X Proteinase K Buffer (50 mL)

Final Conc. of ComponentStockAmount
40 mM Tris-HCl, pH 7.51 M2 mL
40 mM EDTA, pH 8.00.5 M4 mL
2% SDS20%5 mL

Bring final volume to 50 mL with ddH2O in a graduated cylinder. Filter sterilize with syringe filter and store at RT.

 

5X TAE (Tris-Acetic Acid-EDTA) (1 L)

Final Conc. of ComponentStockAmount
200 mM Tris Base24.2 g
100 mM Glacial Acetic Acid17.4 M5.7 mL
5 mM EDTA, pH 8.00.5 M10 mL

Bring final volume to 1 L with ddH2O in a graduated cylinder. Filter sterilize and store at RT.

 

1X TAE (Tris-Acetic Acid-EDTA) (20 L)

Final Conc. of ComponentStockAmount
40 mM Tris Base96.9 g
20 mM Glacial Acetic Acid17.4 M23 mL
1 mM EDTA, pH 8.00.5 M40 mL

Bring final volume to 2 L with ddH2O in a graduated cylinder. Pour into 40 L carboy and add 18 L of ddH2O.

 

5X TBE (Tris/Borate/EDTA) (1 L)

Final Conc. of ComponentStockAmount
445 mM Tris Base53.9 g
445 mM Boric Acid27.5 g
15 mM EDTA, pH 8.00.5 M30 mL

Bring final volume to 1 L with ddH2O in a graduated cylinder. Filter sterilize and store at RT.

 

1X TBE (Tris/Borate/EDTA) (20 L)

Final Conc. of ComponentStockAmount
89 mM Tris Base215.6 g
89 mM Boric Acid110 g
3 mM EDTA, pH 8.00.5 M120 mL

Bring final volume to 2 L with ddH2O in a graduated cylinder. Pour into 40 L carboy and add 18 L of ddH2O.

 

1X TGS (Tris-Glycine-SDS) (20 L)

Final Conc. of ComponentStockAmount
25 mM Tris Base60.6 g
192 mM Glycine288.4 g
0.1% SDS20%100 mL

Bring final volume to 2 L with ddH2O in a graduated cylinder. Pour into 40 L carboy and add 18 L of ddH2O.

 

1X TBST (Tris/buffered saline/Tween-20) (8 L)

Final Conc. of ComponentStockAmount
10 mM Tris Base9.7 g
150 mM NaCl70 g
0.05% Tween-20100%4 mL
HCL1 N40 mL

Bring final volume to 8 L with ddH20 in a graduated cylinder.

 

Complete Protease Inhibitor (EDTA-free) (CPI) (1 mL)

Final Conc. of ComponentStockAmount
Tablets CPI1 Tablet
ddH2O1 mL

Vortex until dissolved. Write the date on the 1.7 mL microcentrifuge tube and store at 4°C for 2 weeks. Throw away the CPI solution after 2 weeks.

 

10% Sodium Deoxycholate (200 mL)

USE MASK--IRRITANT

Final Conc. of ComponentStockAmount
10% Deoxycholic Acid Sodium Salt20 g
Preheated ddH2O200 mL

Prepare in 250 mL glass beaker. Measure the powder into the beaker, and bring final volume to 200 mL with preheated ddH2O. Filter sterilize and store at RT.

 

1 M HEPES-KOH, pH 7.5 (1 L)

Final Conc. of ComponentStockAmount
1 M HEPES238.4 g
KOH1 N500 mL

Add 400 mL of 1 N KOH to start and monitor pH after adding HEPES. Add additional KOH to desired pH endpoint. Bring final volume to 1 L with ddH2O in a graduated cylinder. Filter sterilize and store at RT.

 

20% SDS (Sodium Dodecyl Sulfate) (500 mL)

USE MASK--IRRITANT

20% SDS is typically ordered from Dot Scientific, but separate SDS powder is kept in the lab at the buffer bench.

Final Conc. of ComponentStockAmount
20% SDS100 g
Preheated ddH2O

Start with 300 mL ddH2O in 500 mL glass beaker and heat the water in microwave, then add SDS powder. Bring to 500 mL with ddH2O in a graduated cylinder. Filter sterilize and store at RT.

 

5 M NaCl (1 L)

Final Conc. of ComponentStockAmount
5 M NaCl292.2 g
Preheated ddH2O

Bring final volume to 1 L with ddH2O in a graduated cylinder. Filter sterilize and store at RT. Occasionally, solution will not flow through the filter immediately--allow the solution to cool and it will flow within a minute.

 

2 M KCL (1 L)

Final Conc. of ComponentStockAmount
2 M KCl149.1 g
ddH2O

Bring final volume to 1 L with ddH2O in a graduated cylinder. Filter sterilize and store at RT.

 

25% Triton X-100 (200 mL)

Final Conc. of ComponentStockAmount
25% Triton X-100100%50 mL
Preheated ddH2O

Measure Triton X-100 directly into 250 mL glass beaker. Bring final volume to 200 mL with preheated ddH2O. Let stir on magnetic plate until completely dissolved (up to one hour) Filter sterilize and store at RT.

 

1 M Tris-HCl, pH 7.5 (1 L)

Final Conc. of ComponentStockAmount
1 M Tris Base121.2 g
HCl1 N800 mL

Confirm pH with meter and adjust as needed. Bring final volume to 1 L with ddH2O in a graduated cylinder.

 

1 M Tris-HCl, pH 8.0 (1 L)

Final Conc. of ComponentStockAmount
1 M Tris Base121.2 g
HCl1 N500 mL

Confirm pH with meter and adjust as needed. Bring final volume to 1 L with ddH2O in a graduated cylinder.

 

10% IGEPAL (Chemically indistinct from NP-40) (200 mL)

Final Conc. of ComponentStockAmount
10% IGEPAL100%20 mL
Preheated ddH2O

Measure IGEPAL in a 250 mL glass beaker. Bring final volume to 200 mL with preheated ddH2O. Filter sterilize and store at RT.

 

1 M LiCl (1 L)

Final Conc. of ComponentStockAmount
1 M LiCl42.39 g

Bring final volume to 1 L with ddH2O in a graduated cylinder. Filter sterilize and store at RT.

 

0.5 M EDTA (Ethylenediaminetetraacetic acid), pH 8.0 (500 mL)

Final Conc. of ComponentStockAmount
0.5 M EDTA93.1 g
NaOH (Pellets)~10 g

Add EDTA to 350 mL of ddH2O (EDTA will not dissolve until a certain pH is reached). Add half of the NaOH pellets and allow them to dissolve. Use the pH meter to monitor continuously, adding a few pellets at a time until the pH reaches 8.0. Bring final volume to 500 mL in a graduated cylinder. Filter sterilize and store at RT.

 

1 N HCl (1 L)

Final Conc. of ComponentStockAmount
1 N HCl37%83.3 mL

Bring final volume to 1 L with ddH2O in a graduated cylinder. Store at RT in a glass bottle in the acids cabinet.

 

100 mM PMSF (Phenylmethane sulfonyl fluoride) (10 mL)

HIGHLY TOXIC--WEAR A MASK

Final Conc. of ComponentStockAmount
100 mM PMSF0.174 g
EtOH100%10 mL

Prepare in a 15 mL conical tube. Store at -20°C.

 

3 M Sodium Acetate (50 mL)

Final Conc. of ComponentStockAmount
3 M Sodium Acetate, Anhydrous12.3 g
Glacial Acetic Acid4.3 mL
ddH2O20 mL

Adjust volume to 40 mL. Confirm pH 5.2 with pH meter and adjust with glacial acetic acid if necessary. Bring final volume to 50 mL with ddH2O in graduated cylinder. Filter sterilize and store at RT.

 

0.1% Tween-20 (1 L)

Final Conc. of ComponentStockAmount
0.1% Tween-20100%1 mL
ddH2O999 mL

Add 1 mL of Triton to a 1 L graduated cylinder and bring final volume to 1 L with ddH2O. Filter sterilize and store at RT.


Yeast Harvest and Sonication Solutions

YPD (Yeast Peptone Dextrose) Media (1 L)

ComponentStockAmount
Yeast Extract10 g
Bacto Peptone20 g
Dextrose20 g

Add 700 mL of dH2O to a 2 L beaker and add each of the powders sequentially. Bring up to 1 L with dH2O and autoclave for 20 minutes on liquid cycle in a glass bottle. Store at RT.

 

YPD Media Plates (1 L)

ComponentStockAmount
Yeast Extract10 g
Bacto Peptone20 g
Dextrose20 g
Bacto Agar20 g

Add 700 mL of dH2O to a 2 L beaker and add each of the powders sequentially. Bring up to 1 L with dH2O and autoclave for 20 minutes on liquid cycle in a glass bottle. Pour media into plates when media cools to ~60°C (tolerable to touch for several seconds on bare hand).

 

CSM (Complete Supplement Mixture) His- Media (1 L)

ComponentStockAmount
Yeast Nitrogen Base6.7 g
Dextrose20 g
CSM His-0.77 g
Adenine (Hemisulfate)0.04 g

Add 700 mL of dH2O to a 2 L beaker and add each of the powders sequentially. Bring up to 1 L with dH2O and autoclave for 20 minutes on liquid cycle in a glass bottle. Store at RT.

 

2.5 M Glycine (1 L)

Final Conc. of ComponentStockAmount
2.5 M Glycine187.5 g

Preheat 700 mL ddH2O in a 1 L glass beaker. Pour in powder and let dissolve. Bring final volume to 1 L with ddH2O in a graduated cylinder. Filter sterilize and store at RT.

 

ST Buffer (1 L)

Final Conc. of ComponentStockAmount
10 mM Tris-HCl, pH 7.51 M10 mL
100 mM NaCl5 M20 mL

Bring final volume to 1 L with ddH2O in a graduated cylinder. Filter sterilize and store at 4°C.

 

FA Lysis Buffer (1 L)

Final Conc. of ComponentStockAmount
50 mM HEPES-KOH, pH 7.51 M50 mL
150 mM NaCl5 M30 mL
2 mM EDTA, pH 8.00.5 M4 mL
0.1% Sodium Deoxycholate10%10 mL
1% Triton X-10025%40 mL

Bring volume up to 1 L with ddH2O in a graduated cylinder. Filter sterilize and store at 4˚C.

 

10 mM Hydrogen Peroxide (100 mL)

Final Conc. of ComponentStockAmount
10 mM 30% H2O29.7 M102 μL

Add to 100mL of ddH2O


Mammalian Harvest and Sonication Solutions

Complete Iscove's Modified Dulbecco's Medium (IMDM) (1.11 L)

Final Conc. of ComponentStockAmount
IMDM1X1000 mL
1% Penicillin-Streptomycin10,000 U/mL10 mL
10% Fetal Bovine Serum (FBS)100%100 mL

Note: Procedure below prepares enough media for one full week of passaging and harvesting at 3 L scale K562 cell culture. Adjust number of media bottles to prepare as necessary.

Turn on the UV light in the biological safety cabinet and thaw 2 FBS bottles and 1 Penicillin-Streptomycin bottle in a 37°C water bath for 30 minutes.

After 30 minutes, obtain 10 IMDM bottles. Wipe down all bottles, one serological pipette, a 50 mL serological pipette tip, and a 10 mL serological pipette tip with 70% ethanol, and place under the hood. Add each component to the IMDM carefully without placing lids on surface of hood. Cap the IMDM bottles and label them with a sharpie with the date and contents (10% FBS, 1% Pen/Strep). Store at 4˚C until needed.

Pour 10% bleach in the empty FBS and Pen/Strep bottles and let incubate for 30 minutes. Wipe down the surface of the biological safety hood with 70% ethanol and turn on UV light for 30 minutes. Decant the solutions in FBS and Pen/Strep bottles in sink after 30 minutes.

 

Complete Dulbecco's Modified Eagle Medium (DMEM) (1.11 L)

Final Conc. of ComponentStockAmount
DMEM1X1000 mL
1% Penicillin-Streptomycin10,000 U/mL10 mL
10% Fetal Bovine Serum (FBS)100%100 mL

Turn on the UV light in the biological safety cabinet and thaw 1 FBS bottle and 1 Penicillin-Streptomycin bottle in a 37°C water bath for 30 minutes.

After 30 minutes, obtain 2 DMEM bottles. Wipe down all bottles, one serological pipette, a 50 mL serological pipette tip, and a 10 mL serological pipette tip with 70% ethanol, and place under the hood. Add each component to the DMEM carefully without placing lids on surface of hood. Cap the DMEM bottles and label them with a sharpie with the date and contents (10% FBS, 1% Pen/Strep). Store at 4˚C until needed.

Pour 10% bleach in any empty FBS and Pen/Strep bottles and let incubate for 30 minutes. Wipe down the surface of the biological safety hood with 70% ethanol and turn on UV light for 30 minutes. Decant the solutions in FBS and Pen/Strep bottles in sink after 30 minutes.

 

Complete Roswell Park Memorial Institute (RPMI) 1640 Medium (1.11 L)

Final Conc. of ComponentStockAmount
RPMI 16401X1000 mL
1% Penicillin-Streptomycin10,000 U/mL10 mL
10% Heat-Inactivated Fetal Bovine Serum (FBS)100%100 mL
10 µM 2-Mercaptoethanol55 mM202 µL

Thaw 2 FBS bottles in a 37°C water bath for 30 minutes.

After the FBS is thawed, turn on the UV light in the biological safety cabinet, heat-inactivate the 2 FBS bottles in a 56°C water bath for 30 minutes, and thaw 1 Penicillin-Streptomycin bottle in a 37°C water bath for 30 minutes.

After 30 minutes, obtain 10 RPMI bottles and one bottle of 2-Mercaptoethanol. Wipe down all bottles, one serological pipette, a 50 mL serological tip, a 10 mL serological tip, a p200 pipette and a p200 tip box with 70% ethanol, and place under the hood.

Add each component, except for 2-Mercaptoethanol, to the RPMI 1640 bottles carefully without placing lids on surface of hood. Only add 2-Mercaptoethanol to the first bottle of media you need on that day. Cap the RPMI 1640 bottles and label them with a sharpie with the date and contents (10% FBS, 1% Pen/Strep, 10 µM 2-Mercaptoethanol for the first bottle, and 10% FBS, 1% Pen/Strep for the others). Store at 4˚C until needed.

Pour 10% bleach in any empty FBS and Pen/Strep bottles and let incubate for 30 minutes. Wipe down the surface of the biological safety hood with 70% ethanol and turn on UV light for 30 minutes. Decant the solutions in FBS and Pen/Strep bottles in sink after 30 minutes.

 

3 M Tris-HCl, pH 7.8 (4 L)

Final Conc. of ComponentStockAmount
1 M Tris Base1454.4 g
HCl37%550 mL

Confirm pH with meter and adjust as needed. Bring final volume to 4 L with ddH2O in a graduated cylinder. Filter sterilize and store in 1 L glass bottles.

 

Modified Farnham Lysis Buffer (2 L)

Final Conc. of ComponentStockAmount
20 mM Tris-HCl, pH 8.01 M40 mL
85 mM KCl2 M85 mL
0.5% IGEPAL10%100 mL
0.5% Triton X-10025%40 mL

Bring final volume to 2 L with ddH2O in a graduated cylinder. Filter sterilize and store at 4°C. Record conductivity reading in buffer log folder.

QC Conductivity Reading: 12 (+/-2) mS/cm

 

Nuclear Lysis Buffer -- RIPA Variant (2 L)

Final Conc. of ComponentStockAmount
1X PBS10X200 mL
1% IGEPAL10%200 mL
0.5% Sodium Deoxycholate10%100 mL
0.1% SDS20%10 mL

Bring final volume to 2 L with ddH2O in a graduated cylinder. Filter sterilize and store at 4°C. Record conductivity reading in buffer log folder.

QC Conductivity Reading: 16 (+/-1) mS/cm

 

1X PBS (1 L)

Purchased from Thermo Fisher Scientific, but can also be made as a dilution from 10X PBS. Components and gram amounts shown below for convenience and knowledge purposes.

Final Conc. of ComponentMW (g/mol)Amount
2.7 mM KCl74.550.2 g
1.47 mM KH2PO4 (monobasic)136.090.2 g
137.9 mM NaCl58.448 g
8.1 mM Na2HPO4 (dibasic)141.961.15 g

 

10 mM Tris-HCl, pH 8.0 + 150 mM NaCl (2 L)

Final Conc. of ComponentStockAmount
10 mM Tris-HCl, pH 8.01 M20 mL
150 mM NaCl5 M60 mL

QC: Adjust pH using HCl if above 8.0.

Bring final volume to 2 L with ddH2O in a graduated cylinder. Filter sterilize and store at 4°C.


ChIP Solutions

IP Dilution Buffer (2 L)

Final Conc. of ComponentStockAmount
20 mM Tris-HCl, pH 8.01 M40 mL
2 mM EDTA, pH 8.00.5 M8 mL
150 mM NaCl5 M60 mL
1% Triton X-10025%80 mL

Bring volume up to 2 L with ddH2O. Filter sterilize and store at 4°C.

 

FA Lysis Buffer (2 L)

Final Conc. of ComponentStockAmount
50 mM HEPES-KOH, pH 7.51 M100 mL
150 mM NaCl5 M60 mL
2 mM EDTA, pH 8.00.5 M8 mL
0.1% Sodium Deoxycholate10%20 mL
1% Triton X-10025%80 mL

Bring volume up to 2 L with ddH2O in a graduated cylinder. Filter sterilize and store at 4˚C. Record conductivity reading in buffer log folder.

QC Conductivity Reading: 18.5(+/-1) mS/cm

 

NaCl Buffer 250 (2 L)

Final Conc. of ComponentStockAmount
50 mM HEPES-KOH, pH 7.51 M100 mL
250 mM NaCl5 M100 mL
2 mM EDTA, pH 8.00.5 M8 mL
1% Triton X-10025%80 mL
0.1% Sodium Deoxycholate10%20 mL

Bring volume up to 2 L with ddH2O in a graduated cylinder. Filter sterilize and store at 4˚C. Record conductivity reading in buffer log folder.

QC Conductivity Reading: 25(+/-2) mS/cm

 

LiCl Buffer 250 (2 L)

Final Conc. of ComponentStockAmount
100 mM Tris-HCl, pH 8.01 M200 mL
250 mM LiCl1 M500 mL
1% IGEPAL10%200 mL
1% Sodium Deoxycholate10%200 mL

Bring volume up to 2 L with ddH2O in a graduated cylinder. Filter sterilize and store at 4˚C. Record conductivity reading in buffer log folder.

QC Conductivity Reading: 25(+/-2) mS/cm

 

10 mM Tris-HCl, pH 8.0 (2 L)

Final Conc. of ComponentStockAmount
10 mM Tris-HCl, pH 8.01 M20 mL

Bring volume up to 2 L with ddH2O in a graduated cylinder. Filter sterilize and store at 4˚C. Record pH reading in buffer log folder.

QC pH Reading: 8.0

 

ChIP Elution Buffer (50 mL)

Final Conc. of ComponentStockAmount
25 mM Tris-HCl, pH 7.51 M1.25 mL
2 mM EDTA, pH 8.00.5 M0.2 mL
200 mM NaCl5 M2 mL
0.5% SDS20%1.25 mL

Bring final volume up to 50 mL with ddH2O in a graduated cylinder. Filter sterilize with syringe filter and store at RT. Record pH and conductivity reading in buffer log folder.

QC pH Reading: 8.0

QC Conductivity Reading: 23 (+/-1) mS/cm