Endy:E. coli Western Blot

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modification of Chris Farrell’s protocol
modification of Chris Farrell’s protocol
==Sample preparation==
==Sample preparation==
-
#Start new culture at OD 0.02 from an exponentially growing culture when it reaches ~0.4 OD.
+
*Start new culture at OD 0.02 from an exponentially growing culture when it reaches ~0.4 OD.
-
#Around OD 1.0, take your sample.  Alternatively, sample from chemostat.  Remember to record OD.
+
*At desired OD, take your sample.  Alternatively, sample from chemostat.  Remember to record OD.
-
#Pull 1 mL of culture.
+
*Pull 1 mL of culture.
-
#Immediately spin the cells 13 K (max on table top centrifuge) for 2 minutes to pellet.   
+
*Immediately spin the cells 13 K (max on table top centrifuge) for 2 minutes to pellet.   
-
#Resuspend cells in lysis buffer.
+
*Resuspend cells in lysis buffer.
-
#Final cell concentration will be 2 E6 cells/uL (use OD/cfu curve). Cell lysates can be frozen at this point (-20 C).  Aliquot if desired.
+
*Final cell concentration will be 2 E6 cells/uL (use OD/cfu curve). This concentration is about right for MC4100-pSB4A3.I7101; adjust as necessary.
 +
*Cell lysates can be frozen at this point (-20 C).  Aliquot if desired.
==Gel Preparation==
==Gel Preparation==
see tric-tricine acrylamide gel protocol for pouring vertical acrylamide gels
see tric-tricine acrylamide gel protocol for pouring vertical acrylamide gels
-
#Boil samples for 10 minutes (use 95 C sand block).
+
*Boil samples for 10 minutes (use 95 C sand block).
-
#Spin at 13 K for 10 minutes.
+
*Spin at 13 K for 10 minutes.
*Run 1 E7 cells per lane (5 uL of lysis sup’n and 5 uL of 2X sample buffer).   
*Run 1 E7 cells per lane (5 uL of lysis sup’n and 5 uL of 2X sample buffer).   
*Run GFPssrA standards (10 ng, 20 ng, 40 ng, 60 ng, 80 ng) in water (or neg. control sup’n) to a volume of 5 uL mixed with 5 uL 2X sample buffer.   
*Run GFPssrA standards (10 ng, 20 ng, 40 ng, 60 ng, 80 ng) in water (or neg. control sup’n) to a volume of 5 uL mixed with 5 uL 2X sample buffer.   
(20.8 ng/uL GFP-SsrA aliquots at –80C; keep on ice until use)
(20.8 ng/uL GFP-SsrA aliquots at –80C; keep on ice until use)
*Run 3 uL Amersham Rainbow marker #755 as size marker (gfp runs w/ orange band).  
*Run 3 uL Amersham Rainbow marker #755 as size marker (gfp runs w/ orange band).  
-
#Mix samples and standards with 2X sample buffer (in pcr tubes) and boil 10 minutes (95 C heat block).  Spin down and load onto tric-tricine acrylamide gel (see JcBAcrylGel_protocol) immediately.
+
*Mix samples and standards with 2X sample buffer (in pcr tubes) and boil 10 minutes (95 C heat block).  Spin down and load onto tric-tricine acrylamide gel (see JcBAcrylGel_protocol) immediately.
[1 E7 cell/lane is good for pSB4A3.I7101.  Adjust for higher or lower expression levels]
[1 E7 cell/lane is good for pSB4A3.I7101.  Adjust for higher or lower expression levels]
==Transfer and Incubations==
==Transfer and Incubations==
-
#After running gel, cut away stacking gel, cut a corner to mark orientation, and soak in transfer buffer for 45 minutes.
+
*After running gel, cut away stacking gel, cut a corner to mark orientation, and soak in transfer buffer for 45 minutes.
-
#Cut PVDF and 3mm Whatman blotting paper to correct size (about 8.5cm X 5cm for PVDF, blotting paper can be a bit larger)
+
*Cut PVDF and 3mm Whatman blotting paper to correct size (about 8.5cm X 5cm for PVDF, blotting paper can be a bit larger)
-
#Cut corner on PVDF and wet with methanol, then soak 5 minutes in H20, followed by 10 minutes in transfer buffer.  Wet 4 pieces of blotting paper in transfer buffer.
+
*Cut corner on PVDF and wet with methanol, then soak 5 minutes in H20, followed by 10 minutes in transfer buffer.  Wet 4 pieces of blotting paper in transfer buffer.
-
#Set up transfer bottom to top: 2 pieces blotting paper, gel, PVDF, two pieces blotting paper.  Be sure to preserve orientation of blot and avoid bubbles.
+
*Set up transfer bottom to top: 2 pieces blotting paper, gel, PVDF, two pieces blotting paper.  Be sure to preserve orientation of blot and avoid bubbles.
-
#Transfer 2 mA/cm^2 until transfer is complete (i.e. rainbow marker is fully transferred to PVDF membrane).  For one 8.5 X 5 blot, this works out to 85 mA for about 2 hours.
+
*Transfer 2 mA/cm^2 until transfer is complete (i.e. rainbow marker is fully transferred to PVDF membrane).  For one 8.5 X 5 blot, this works out to 85 mA for about 2 hours.
-
#Block membrane for 1 hr with 5% milk/TBS-Tween (0.1 %).  Use the lid of a pipette tip box and 15 mL fluid to cover blot. (for two blots, use a large tip box and 25 mL fluid for all incubations/washes) Place blot on shaker table for all incubations.
+
*Block membrane for 1 hr with 5% milk/TBS-Tween (0.1 %).  Use the lid of a pipette tip box and 15 mL fluid to cover blot. (for two blots, use a large tip box and 25 mL fluid for all incubations/washes) Place blot on shaker table for all incubations.
-
#Incubate overnight with 1:10000 dilution of anti-GFP in 2% milk/TBS-Tween (0.1%)
+
*Incubate overnight with 1:10000 dilution of anti-GFP in 2% milk/TBS-Tween (0.1%)
-
#Wash 3X in 15 mL TBS-Tween (0.1%) for 10 minutes.
+
*Wash 3X in 15 mL TBS-Tween (0.1%) for 10 minutes.
-
#Incubate 30 minutes with 1:10000 dilution of ECF secondary antibody in TBS-Tween (0.1%)
+
*Incubate 30 minutes with 1:10000 dilution of ECF secondary antibody in TBS-Tween (0.1%)
-
#Wash 3X in 15 mL TBS-Tween (0.1%) for 10 minutes.
+
*Wash 3X in 15 mL TBS-Tween (0.1%) for 10 minutes.
==Analyzing Western==
==Analyzing Western==
-
#Turn on Fluorimager 30 minutes before use.  Put in 570 filter.
+
*Turn on Fluorimager 30 minutes before use.  Put in 570 filter.
-
#Settings are  PVDF 488/570 df 30, PMT = 500.  Select area to scan.
+
*Settings are  PVDF 488/570 df 30, PMT = 500.  Select area to scan.
-
#Place 1 mL of ECF substrate on a transparency.  ECF substrate in buffer is stored in 1 mL aliquots at –80C.
+
*Place 1 mL of ECF substrate on a transparency.  ECF substrate in buffer is stored in 1 mL aliquots at –80C.
-
#Using forceps, lay blot face down on top of substrate (no bubbles) for about one minute (less if bands become visible).  Transfer blot face down to fluorimager plate.  
+
*Using forceps, lay blot face down on top of substrate (no bubbles) for about one minute (less if bands become visible).  Transfer blot face down to fluorimager plate.  
-
#Insert plate into machine.  Scan image.  Remove plate immediately.
+
*Insert plate into machine.  Scan image.  Remove plate immediately.
-
#Remove plate before shutting down scanner.  Leave software open if anyone is signed up within two hours.
+
*Remove plate before shutting down scanner.  Leave software open if anyone is signed up within two hours.
-
#Clean plate with dI and kim wipes, then with ethanol from the glass bottle.  Return plates to cabinet across hall.
+
*Clean plate with dI and kim wipes, then with ethanol from the glass bottle.  Return plates to cabinet across hall.
==Quantification in ImageQuant==
==Quantification in ImageQuant==
-
#Use rectangle tool to draw object around band.  Copy and paste object so that all objects have the same area.
+
*Use rectangle tool to draw object around band.  Copy and paste object so that all objects have the same area.
-
#It is not necessary to define a background in ImageQuant.  Do volume report without background correction, and set the negative control equal to 0 ng/lane for your standard curve.
+
*It is not necessary to define a background in ImageQuant.  Do volume report without background correction, and set the negative control equal to 0 ng/lane for your standard curve.
-
#Double click report to make it an excel file and save images and excel.
+
*Double click report to make it an excel file and save images and excel.
-
#Alternatively, make a new object to define background and set background on all lanes equal to “object ave” for this object. (analyze>>”background correction” to set background correction, then analyze>>”volume report”) (“local average” sets background equal to the average pixel value of the object perimeter.  This will be problematic if bands are not well separated.)   
+
*Alternatively, make a new object to define background and set background on all lanes equal to “object ave” for this object. (analyze>>”background correction” to set background correction, then analyze>>”volume report”) (“local average” sets background equal to the average pixel value of the object perimeter.  This will be problematic if bands are not well separated.)   
volume = (average pixel value – background value) * object area
volume = (average pixel value – background value) * object area
-
#Use standards to estimate ng gfp/lane for samples and calculate gfp/cell.  The    molecular weight of GFP-SsrA is about 28.3 kDa.
+
*Use standards to estimate ng gfp/lane for samples and calculate gfp/cell.  The    molecular weight of GFP-SsrA is about 28.3 kDa.
==2X Tricine Sample Buffer==
==2X Tricine Sample Buffer==
-
2 mL 4X Tris-Cl/SDS, pH 8.8
+
*2 mL 4X Tris-Cl/SDS, pH 8.8
-
6 mL 40% glycerol (24% final)
+
*6 mL 40% glycerol (24% final)
-
0.8 g SDS (8% final)
+
*0.8 g SDS (8% final)
-
0.31 g DTT (0.2 M final)
+
*0.31 g DTT (0.2 M final)
-
2 mg Coomassie blue G-250 (0.02% final) (used C. Blue G)
+
*2 mg Coomassie blue G-250 (0.02% final) (used C. Blue G)
-
to 10 mL with MilliQ H2O and mix
+
*to 10 mL with MilliQ H2O and mix
-
aliquot 500 uL/tube and store at –20 C
+
*aliquot 500 uL/tube and store at –20 C
==4X Tris-Cl/SDS pH 8.8==
==4X Tris-Cl/SDS pH 8.8==
-
91 g Tris
+
*91 g Tris
-
dissolve in 300 mL H2O
+
*dissolve in 300 mL H2O
-
pH to 8.8 with 1N HCl (about 120 mL)
+
*pH to 8.8 with 1N HCl (about 120 mL)
-
to 500 mL with H2O
+
*to 500 mL with H2O
-
filter 0.45 um
+
*filter 0.45 um
-
add 2g SDS and store 4 C
+
*add 2g SDS and store 4 C
==Lysis Buffer  (12.5 mM Tris pH 6.8, 4% SDS==
==Lysis Buffer  (12.5 mM Tris pH 6.8, 4% SDS==
-
1.25 mL 1M Tris (pH 8)
+
*1.25 mL 1M Tris (pH 8)
-
to 80 mL with st. H2O
+
*to 80 mL with st. H2O
-
pH if necessary  
+
*pH if necessary  
-
to 100 mL with st. H2O
+
*to 100 mL with st. H2O
-
add 4g SDS
+
*add 4g SDS
==TBS-Tween (0.1%)==
==TBS-Tween (0.1%)==
-
100 mL 10X TBS
+
*100 mL 10X TBS
-
900 mL H2O
+
*900 mL H2O
-
1 mL Tween (Polyoxyethylene sorbitan monolaurate)
+
*1 mL Tween (Polyoxyethylene sorbitan monolaurate)
-
10X TBS (500 mM Tris, 1.5 M NaCl)
+
*10X TBS (500 mM Tris, 1.5 M NaCl)
-
150 mL 5M NaCl
+
**150 mL 5M NaCl
-
250 mL 1M Tris, pH 7.5
+
**250 mL 1M Tris, pH 7.5
-
to 500 mL with H2O
+
**to 500 mL with H2O
==1M Tris-Cl, pH 8 (or 7.5)==
==1M Tris-Cl, pH 8 (or 7.5)==
-
121 g tris base
+
*121 g tris base
-
700 mL MilliQ H2O
+
*700 mL MilliQ H2O
-
to pH 8 with 6N HCl (about 100 mL)
+
*to pH 8 with 6N HCl (about 100 mL)
-
to 1 L with MilliQ H2O
+
*to 1 L with MilliQ H2O
-
filter 0.45 um or autoclave (fluid, 20 psi, 250 F, 20 min)
+
*filter 0.45 um or autoclave (fluid, 20 psi, 250 F, 20 min)
==Transfer Buffer (“Towbin Buffer”)==
==Transfer Buffer (“Towbin Buffer”)==
-
3 g Tris
+
*3 g Tris
-
14.4 g glycine
+
*14.4 g glycine
-
800 mL dI
+
*800 mL dI
-
200 mL methanol
+
*200 mL methanol
note: anti-GFP is Assay Designs 915-059, rabbit (store one aliquot at 4 C to avoid freeze/thaw, rest at –20C)
note: anti-GFP is Assay Designs 915-059, rabbit (store one aliquot at 4 C to avoid freeze/thaw, rest at –20C)
ECF Western Blotting kit is Amersham RPN5783 (rabbit)
ECF Western Blotting kit is Amersham RPN5783 (rabbit)
To connect to Bionet from fluorimager: \\18.79.1.147\endy    DNA-NET\username
To connect to Bionet from fluorimager: \\18.79.1.147\endy    DNA-NET\username

Revision as of 22:43, 25 July 2005

Contents

GFP Quantitative Western

JCB Protocol for plasmid based GFP; batch or chemostat culture modification of Chris Farrell’s protocol

Sample preparation

  • Start new culture at OD 0.02 from an exponentially growing culture when it reaches ~0.4 OD.
  • At desired OD, take your sample. Alternatively, sample from chemostat. Remember to record OD.
  • Pull 1 mL of culture.
  • Immediately spin the cells 13 K (max on table top centrifuge) for 2 minutes to pellet.
  • Resuspend cells in lysis buffer.
  • Final cell concentration will be 2 E6 cells/uL (use OD/cfu curve). This concentration is about right for MC4100-pSB4A3.I7101; adjust as necessary.
  • Cell lysates can be frozen at this point (-20 C). Aliquot if desired.


Gel Preparation

see tric-tricine acrylamide gel protocol for pouring vertical acrylamide gels

  • Boil samples for 10 minutes (use 95 C sand block).
  • Spin at 13 K for 10 minutes.
  • Run 1 E7 cells per lane (5 uL of lysis sup’n and 5 uL of 2X sample buffer).
  • Run GFPssrA standards (10 ng, 20 ng, 40 ng, 60 ng, 80 ng) in water (or neg. control sup’n) to a volume of 5 uL mixed with 5 uL 2X sample buffer.

(20.8 ng/uL GFP-SsrA aliquots at –80C; keep on ice until use)

  • Run 3 uL Amersham Rainbow marker #755 as size marker (gfp runs w/ orange band).
  • Mix samples and standards with 2X sample buffer (in pcr tubes) and boil 10 minutes (95 C heat block). Spin down and load onto tric-tricine acrylamide gel (see JcBAcrylGel_protocol) immediately.

[1 E7 cell/lane is good for pSB4A3.I7101. Adjust for higher or lower expression levels]

Transfer and Incubations

  • After running gel, cut away stacking gel, cut a corner to mark orientation, and soak in transfer buffer for 45 minutes.
  • Cut PVDF and 3mm Whatman blotting paper to correct size (about 8.5cm X 5cm for PVDF, blotting paper can be a bit larger)
  • Cut corner on PVDF and wet with methanol, then soak 5 minutes in H20, followed by 10 minutes in transfer buffer. Wet 4 pieces of blotting paper in transfer buffer.
  • Set up transfer bottom to top: 2 pieces blotting paper, gel, PVDF, two pieces blotting paper. Be sure to preserve orientation of blot and avoid bubbles.
  • Transfer 2 mA/cm^2 until transfer is complete (i.e. rainbow marker is fully transferred to PVDF membrane). For one 8.5 X 5 blot, this works out to 85 mA for about 2 hours.
  • Block membrane for 1 hr with 5% milk/TBS-Tween (0.1 %). Use the lid of a pipette tip box and 15 mL fluid to cover blot. (for two blots, use a large tip box and 25 mL fluid for all incubations/washes) Place blot on shaker table for all incubations.
  • Incubate overnight with 1:10000 dilution of anti-GFP in 2% milk/TBS-Tween (0.1%)
  • Wash 3X in 15 mL TBS-Tween (0.1%) for 10 minutes.
  • Incubate 30 minutes with 1:10000 dilution of ECF secondary antibody in TBS-Tween (0.1%)
  • Wash 3X in 15 mL TBS-Tween (0.1%) for 10 minutes.

Analyzing Western

  • Turn on Fluorimager 30 minutes before use. Put in 570 filter.
  • Settings are PVDF 488/570 df 30, PMT = 500. Select area to scan.
  • Place 1 mL of ECF substrate on a transparency. ECF substrate in buffer is stored in 1 mL aliquots at –80C.
  • Using forceps, lay blot face down on top of substrate (no bubbles) for about one minute (less if bands become visible). Transfer blot face down to fluorimager plate.
  • Insert plate into machine. Scan image. Remove plate immediately.
  • Remove plate before shutting down scanner. Leave software open if anyone is signed up within two hours.
  • Clean plate with dI and kim wipes, then with ethanol from the glass bottle. Return plates to cabinet across hall.

Quantification in ImageQuant

  • Use rectangle tool to draw object around band. Copy and paste object so that all objects have the same area.
  • It is not necessary to define a background in ImageQuant. Do volume report without background correction, and set the negative control equal to 0 ng/lane for your standard curve.
  • Double click report to make it an excel file and save images and excel.
  • Alternatively, make a new object to define background and set background on all lanes equal to “object ave” for this object. (analyze>>”background correction” to set background correction, then analyze>>”volume report”) (“local average” sets background equal to the average pixel value of the object perimeter. This will be problematic if bands are not well separated.)

volume = (average pixel value – background value) * object area

  • Use standards to estimate ng gfp/lane for samples and calculate gfp/cell. The molecular weight of GFP-SsrA is about 28.3 kDa.


2X Tricine Sample Buffer

  • 2 mL 4X Tris-Cl/SDS, pH 8.8
  • 6 mL 40% glycerol (24% final)
  • 0.8 g SDS (8% final)
  • 0.31 g DTT (0.2 M final)
  • 2 mg Coomassie blue G-250 (0.02% final) (used C. Blue G)
  • to 10 mL with MilliQ H2O and mix
  • aliquot 500 uL/tube and store at –20 C

4X Tris-Cl/SDS pH 8.8

  • 91 g Tris
  • dissolve in 300 mL H2O
  • pH to 8.8 with 1N HCl (about 120 mL)
  • to 500 mL with H2O
  • filter 0.45 um
  • add 2g SDS and store 4 C

Lysis Buffer (12.5 mM Tris pH 6.8, 4% SDS

  • 1.25 mL 1M Tris (pH 8)
  • to 80 mL with st. H2O
  • pH if necessary
  • to 100 mL with st. H2O
  • add 4g SDS

TBS-Tween (0.1%)

  • 100 mL 10X TBS
  • 900 mL H2O
  • 1 mL Tween (Polyoxyethylene sorbitan monolaurate)
  • 10X TBS (500 mM Tris, 1.5 M NaCl)

**150 mL 5M NaCl **250 mL 1M Tris, pH 7.5 **to 500 mL with H2O

1M Tris-Cl, pH 8 (or 7.5)

*121 g tris base *700 mL MilliQ H2O *to pH 8 with 6N HCl (about 100 mL) *to 1 L with MilliQ H2O

  • filter 0.45 um or autoclave (fluid, 20 psi, 250 F, 20 min)

Transfer Buffer (“Towbin Buffer”)

  • 3 g Tris
  • 14.4 g glycine
  • 800 mL dI
  • 200 mL methanol

note: anti-GFP is Assay Designs 915-059, rabbit (store one aliquot at 4 C to avoid freeze/thaw, rest at –20C) ECF Western Blotting kit is Amersham RPN5783 (rabbit) To connect to Bionet from fluorimager: \\18.79.1.147\endy DNA-NET\username

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