Western Blot Experiment Log

Use orange color to indicate ongoing experiments that should not be forgotten.
Use red color to indicate noteworthy problems encountered.
Use green color to highligt important conclusions or questions.
 
Date Laborator Experiment short name Experiment details
Buffer
Tissue
Gel type Antibodies (pri/sec dilution) Results (specific signal, background) Problems Conclusions
 020625 MAL/EED Establishing standard protocol-Extractions Trizol and lysis buffer (Na-Acetate + Triton) protein extractions and BSA standards.  NaAc/Mu - - BSA standards plot  -  -
020729 MAL/EED Establishing standard protocol-Extractions Trizol extraction NaAc/Mu - - No pellet! Phases separated incorrectly, red phase up and aqeus phase down -
020730 MAL/EED Establishing standard protocol-Extractions Detergent lysis using Na-Acetate buffer NaAc/Mu - - Abundant protein extracted without problems. Aliquots prepared and stored at -70ºC - Worked correctly, gave good yield: 9,9mg protein from 148mg tissue (0,067mg protein/mg tissue)
020801 MAL/EED Testing anti-GFAP Establishing standard protocol, on 25, 50 and 100µg protein from 020730. NaAc/Mu 8% Tris-Glycine GFAP mo: 1:15000. HRP-conj-anti-Mo 1:1500. Band of correct size identified using 25, 50 and 100µg protein. Low background. Weak unspecific bands only at 100µg. Film Marker is unreliable -too weak on gel, weaker on membrane: too old? Very promising results. Nice signal to noise ratio. Na-Acetate lysis buffer extraction works well.
020805 MAL/EED Testing anti-Shc (pan) Establishing standard protocol, on 25, 50 and 100µg protein from 020730. NaAc/Mu 8% Tris-Glycine Shc-mo: 1:1000  (upstate #06-203). HRP-conj-anti-Mo 1:1500. OK. Film Marker is unreliable -too weak on gel, weaker on membrane: too old? -
020807 MAL/EED Testing anti-p75 Establishing standard protocol, on 25, 50 and 100µg protein from 020730. NaAc/Mu 8% Tris-Glycine p75-rb 1:10000  (gift Wesskamp)
HRP-conj-anti-Rb 1:1500
Band visible but size cannot be judged. Marker is unreliable -too weak on gel, weaker on membrane: too old? New marker needed!
020808 MAL/EED SC extraction & testing of anti-Shc (pan) Extraction: rem SC 20/65mg in Na-Acetate lysis buffer. Need to detect p66 isoform. NaAc/SC rem. 8% Tris-Glycine Shc-mo: 1:1000  (upstate #06-203). HRP-conj-anti-Mo 1:1500. 20mg gave 591µg protein (yield of 3%). 65mg gave 1622 µg (yield of 2.5%) - -
020808 MAL/EED Ordering new materials Amersham Biosciences: Full range rainbow MW marker  RPN800; precut 7X8cm Hybond ECL membranes RPN78D; ECL western blot detection system reagents RPN2108. ECL Hyperfilm 18X24cm RPN2103. New marker works nicely.    Use new marker
 020812 MAL/EED Sc & muscle p75 Comparing SC and muscle p75 signals. Loaded amount: 20, 40 and 80 µg protein.  NaAc/SC&Mu  8% Tris-Glycine  p75-rb 1:10000  (gift Wesskamp)
HRP-conj-anti-Rb 1:1500
-  -  -
020812 MAL/EED Ordering new gels Novex precast  Tris-Glycine gels: 12%, 1.5mm, 15well, EC60085. - - - - - -
020814 MAL/EED anti-Shc (pan)  Comparing SC and muscle Shc signals. Loaded amount: 20, 40 and 80 µg protein. NaAc/SC  & Mu 8% Tris-Glycine Shc-mo: 1:1000  (upstate #06-203). HRP-conj-anti-Mo 1:1500. - - -
020819 MAL/EED Molding gels 10% Tris-glycine gels. Agarose 1% used to seal gel casettes. - 10% Tris-Glycine - - - Excellent!
020820 MAL/EED Testing ED2 on home-made gels Loaded amount: 20, 40 and 80 µg protein. ED2 is constitutively expressed in MØ. NaAc/Mu 10% Tris-Glycine ED2-mo 1:5000 (Serotec 1999).HRP-conj-anti-Mo 1:1500. Clear bands, probably specific but size does not match marker. Likely due to samples not being reduced while reducing agent included in marker. - -
020821 MAL/EED Discovering method error No reducing agent included in sample buffer - - - - Unreduced samples will not migrate correctly during electrophoresis. ß-Mercapto-Ethanol should be added to 5% in sample buffer (2X). Final concentration 2.5% when loaded.
020821 MAL/EED Ordering Shc antibodies Ordering Shc pan and p66 specific  antibodies (Rb-Shc-mo: Upstate #06-203) and Rb-p66 Upstate #07-150) via KeLab. -   Rb-Shc: 1:1000
Rb-p66
Positive control included.
- - -
020826 MAL/EED Extracting protein from muscle D11, 15, 18, 28 and yad B1-5 Protein extracted from Gastroc muscle of  D11: 58; D15: 88; D18: 70; D28: 75mg and yad B1: 39; B2: 50; B4: 30; B5: 36mg. Protein extracted in 500µl NaAcetate lysis buffer. Spinning after inc: 25min at max speed 13K G. Aliquots of 5µg/µl prepared and stored in -70ºC upright freezer. NaAc/Mu - - Supernate volumes all about 450µl. - -
020902 MAL/EED Testing p66 spec AB Muscle, SC and positive control samples NaAc/ Mu, SC, PC (10µg) 4-12% wide range gel Rb-p66 Upstate #07-150 - - -
020903 MAL/EED Shc-p66 aliquots prepared  Upstate Rb-p66  #07-150 antibody aliquoted 5µl/tube. Suggested dilution 1:1000-1:2000. Stored in upright -70ºC freezer. - - Rb-p66 Upstate #07-150 - - -
020906 MAL/EED ShcA-pan muscle Mu D18,11,28, Yad + positive control
10, 20, 40 µg protein per lane and animal
NaAc/Mu 4-12% wide range gel PrAb: Rb-Shc: 1:1000
SecAb: HRP-conj-anti-Rb 1:1500.
- - -
020911 MAL/EED p66-ShcA  muscle Mu D18,11,28, Yad + positive control
10, 20, 40 µg protein per lane and animal
NaAc/Mu 4-12% wide range gel PrAb: Rb-p66: 1:1000
SecAb: HRP-conj-anti-Rb 1:1500.
- - p66 antibody does not work very well in Mu, gives a lot of background. optimize?
020912 MAL/EED p66-ShcA  SC SC-Th D18, 11, 28 and yad
10, 20, 40 µg protein per lane and animal
NaAc/Sc 4-12% wide range gel PrAb: Rb-p66: 1:1000
SecAb: HRP-conj-anti-Rb 1:1500.
- - p66 antibody does not work very well in Sc, gives a lot of background. optimize?
020913 MAL/EED ShcA-pan SC
two experiments 
SC-Th D18, 11, 28 and yad
10, 20, 40 µg protein per lane and animal
NaAc/Sc 4-12% wide range gel (2 gels) PrAb: Rb-Shc: 1:1000
SecAb: HRP-conj-anti-Rb 1:1500.
Gel 1 and 2 looks the same, D11 shows strange results - -
020917 MAL/EED ShcA-pan muscle Gastroc muscle D15,18, 11, 28 and yad
10, 20, 40 µg protein per lane and animal
NaAc/Mu 4-12% wide range gel PrAb: Rb-Shc: 1:1000
SecAb: HRP-conj-anti-Rb 1:1500.
- - -
020918 MAL/EED ShcA-pan SC SC-Th D15,18, 11, 28 and yad
10, 20, 40 µg protein per lane and animal
NaAc/Sc 4-12% wide range gel PrAb: Rb-Shc: 1:1000
SecAb: HRP-conj-anti-Rb 1:1500.
D11 is still not good - -
020924 MAL/EED ShcA-pan SC SC-Th D15,18, 11, 28 and yad.
10, 20, 40 µg protein per lane and animal
NaAc/Sc 4-12% wide range gel PrAb: Rb-Shc: 1:1000
SecAb: HRP-conj-anti-Rb 1:1500.
D11 is still not good - -
020926 MAL/EED ShcA-pan SC SC-Th D15,18, 11, 28 pooled and yad with positive control
10, 20, 40 µg protein per lane and pooled animals and Yad
NaAc/Sc 10% Tris-Glycine self-made PrAb: Rb-Shc: 1:1000
SecAb: HRP-conj-anti-Rb 1:1500.
- - -
021001 MAL/EED Testing IGF-1 antibodies Mu, test tissue (m.gastroc) 
25, 50 and 100 µg protein per lane.
NaAc/Mu 15% Tris-Glycine self-made Rb-anti-IGF-1 Peninsula labs # IHC7308. Dil: 1:10 000. Detection HRP-conj-anti-Rb 1:1500.Mo-anti-IGF-1 Upstate #05-172. Sugg. Dil: 1µg/1000µl. From aliquot dil: 1:10 000. Detection HRP-conj-anti-Mo 1:1500. Polyclonal shows a lot of large bands. 40% Cross-R with IGF-2.
Monoclonal shows few and distinct bands. Repeat experiment needed to confirm correctness of sizes (ladder needs to be cut away before blocking). Compare bands at 14 (IGF-1) and 12KD (IGF-2)
-Smiley effect on gel phoresis. Agarose sealing is liquid proof but not electrophoretically inert. Very nice separation in 15% gel. Polyclonal good for identifying IGF-2 in comparison with IGF-1 mono. Extra bands would be nice to confirm as IGF-1 complexed to bp:s.
0210ZZ EED Re-testing IGF-1 antibodies Mu, test tissue (m.gastroc) 
25, 50 and 100 µg protein per lane.
NaAc/Mu 15% Tris-Glycine self-made Rb-anti-IGF-1 Peninsula labs # IHC7308. Dil: 1:10 000. Detection HRP-conj-anti-Rb 1:1500.Mo-anti-IGF-1 Upstate #05-172. Sugg. Dil: 1µg/1000µl. From aliquot dil: 1:10 000. Detection HRP-conj-anti-Mo 1:1500. No results gel run useless.  Migration uneven, heading for side of gel. Agarose does not block electrolyte movement!
021025 EVI Ordering new gel casettes - - - 1.0mm, 1.5mm and 12 lane 1mm combs. - - -
021107
021108
EED Testing IL-6 & retesting IGF-1 antibodies

run+rerun

Mu, test tissue (m.gastroc) 
40, 80 µg protein per lane.
NaAc/Mu 15% Tris-Glycine self-made Goat-anti-IL-6 Santa Cruz #R19, dil 1:1000. Detection Jackson HRP-conj-anti-Go 1:2000. Rb-anti-IGF-1 Peninsula labs # IHC7308. Dil: 1:10 000. Detection HRP-conj-anti-Rb 1:2000.Mo-anti-IGF-1 Upstate #05-172. Sugg. Dil: 1µg/1000µl. From aliquot dil: 1:10 000. Detection HRP-conj-anti-Mo 1:2000. - First run cover left on membrane = no transfer. Second run some of bubbles at transfer. Primary stayed on for too long (2.5h) and backgrounf was immense for the polyclonals but not for the monoclonal. -
021111 EED Retesting IL-6, testing CNTF and FGF-2 Mu, test tissue (m.gastroc)
40, 80 µg protein per lane.
NaAc/Mu 15% Tris-Glycine self-made Goat-anti-IL-6 Santa Cruz #R19, dil 1:1000. Detection Jackson HRP-conj-anti-Go 1:1500. CNTF Chemicon #MAB338 - - We need to prepare more test lysates.
021112 EED Testing CNTF and LIF Mu, test tissue (m.gastroc) 
25, 50 µg protein per lane.
NaAc/Mu 15% Tris-Glycine self-made CNTF Chemicon #MAB338 mo 1:5000/10000; Detection HRP-conj-anti-Mo 1:2000 LIF polyclonal (TH-lab); Detection HRP-conj-anti-Rb 1:5000 - - -
021113 EED IGF-1 mo Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate NaAc/Mu 15% Tris-Glycine self-made Mo-anti-IGF-1 Upstate #05-172. Sugg. Dil: 1µg/1000µl. From aliquot dil: 1:10 000. Detection HRP-conj-anti-Mo 1:2000. - - -
021114 EED IGF-1 Rb Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate NaAc/Mu 15% Tris-Glycine self-made Rb-anti-IGF-1 Peninsula labs # IHC7308. Dil: 1:10 000. Detection HRP-conj-anti-Rb 1:2000 ok - -
021115 EED CNTF mo Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate NaAc/Mu 15% Tris-Glycine self-made CNTF Chemicon #MAB338 mo 1:10000. Detection HRP-conj-anti-Mo 1:2000 Strange results: reverse migration in some lanes?  - -
021217 EED IGF-1 Rb rerun Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate NaAc/Mu 15% Tris-Glycine self-made Rb-anti-IGF-1 Peninsula labs # IHC7308. Dil: 1:10 000. Detection HRP-conj-anti-Rb 1:2000 Not ok Strange result! some samples have reduced total signal -includes background -
030113 EED IGF-1 Rb rerun Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate NaAc/Mu 15% Tris-Glycine self-made Rb-anti-IGF-1 Peninsula labs # IHC7308. Dil: 1:10 000. Detection HRP-conj-anti-Rb 1:2000 ok - -
030114 EED IGF-1 Rb rerun Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate NaAc/Mu 15% Tris-Glycine self-made Rb-anti-IGF-1 Peninsula labs # IHC7308. Dil: 1:10 000. Detection HRP-conj-anti-Rb 1:2000 ok - -
030114 EED CNTF mo Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate NaAc/Mu 15% Tris-Glycine self-made CNTF Chemicon #MAB338 mo 1:10000. Detection HRP-conj-anti-Mo 1:2000 Error in loading exp not completed - -
030129 EED CNTF mo Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate NaAc/Mu 15% Tris-Glycine self-made CNTF Chemicon #MAB338 mo 1:10000. Detection HRP-conj-anti-Mo 1:2000 Nice results! - -
030130 EED CNTF mo & LIF rb Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate. Testing 2ml antibody volume in laminated plastic sheath. NaAc/Mu 15% Tris-Glycine self-made CNTF Chemicon #MAB338 mo 1:10000. Detection HRP-conj-anti-Mo 1:2000. LIF polyclonal 1:10000 Detection HRP-conj-anti-Rb 1:2000 CNTF -as before.
LIF weak bands but looks ok.
Laminating device tricky, sometimes melts, sometimes seals, never perfect! Reuse antibody instead, as suggested by G. Schulte: dilute in buffer + 5%BSA and add NaAz; can be reused several times...
030206 MAL/EED Preparing protocols for phospho-western New extraction protocol: TRIS-base buffer including protease inhibitors and phosphorylation stabilizers. - - - - - -
030207 MAL/EED Protein extraction using phospo-protocol Test tissue: wistar, female 020729, mu gastroc. TRIS-base protocol. TRIS-(p)/Mu - - 6X50µl  33.35µg/µl (yield 21.3 µg/mg) - -
030210 MAL/EED Test: phospho-Akt Phospho-spcific antibody p-Akt tested on mu gastroc test tissue extracted 030207. 300, 200, 100, 50µg loaded. TRIS-(p)/Mu 10% Tris-Glycine self-made p-Akt (Ser473) Cell Signaling #9271 Rb1:1000
Detection HRP-conj-anti-Rb 1:1500
somewhat weak signal: 15min exposure ok but far from saturated - -
030212 EED CNTF mo & LIF rb Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate. Lamination was quite messy; will try to dissolve LIF-ab in PBS containing BSA instead of milk and add some NaAz which should allow reuse of ab. NaAc/Mu 15% Tris-Glycine self-made CNTF Chemicon #MAB338 mo 1:10000. Detection HRP-conj-anti-Mo 1:2000. LIF polyclonal 1:10000 Detection HRP-conj-anti-Rb 1:2000 Gel ruptured before transfer; used for CNTF confirmation run. Weak signals but ok. -
030218 EED LIF rb & IL-6 Go Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate. Protocol change: 45min room temp blocking and  overnight primary Ab incubation NaAc/Mu 15% Tris-Glycine self-made LIF polyclonal 1:10000 Detection HRP-conj-anti-Rb 1:2000. Goat-anti-IL-6 Santa Cruz #R19, dil 1:4000. Detection Jackson HRP-conj-anti-Go 1:2000.  - Weak LIF-signals but ok result. No specific IL-6 bands Overnight incubation with primary not a problem nor an advantage. 45min blocking at RT works -compress protocol..?
030227 EED IL-6 & bFGF test. Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate. Protocol change: 45min room temp blocking and  overnight primary Ab incubation NaAc/Mu 15% Tris-Glycine self-made Goat-anti-IL-6 Santa Cruz #R19, dil 1:4000. Detection Jackson HRP-conj-anti-Go 1:2000. bFGF  () from S.K.s IHC dilutions. Dil: 1:4000. Detection HRP-conj-anti-Rb 1:2000. - - -
030301 EED IL-6 Mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate. Protocol change: 45min room temp blocking and  overnight primary Ab incubation NaAc/Mu 15% Tris-Glycine self-made Goat-anti-IL-6 Santa Cruz #R19, dil 1:4000. Detection Jackson HRP-conj-anti-Go 1:2000.  - messy membrane but results discernable Insufficient wash after primary?
030328 EED IL-6 rerun, bFGF and MyoD-test Weekend prep:
samples for new bFGF antibody test, MyoD-test and new IL-6 run
NaAc/Mu 15% Tris-Glycine self-made - - - -
030329 EED IL-6 rerun, bFGF and MyoD-test IL-6 rerun mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate. bFGF and MyoD-test on yad mu lysate (+D15 for myoD) NaAc/Mu 15% Tris-Glycine self-made Goat-anti-IL-6 Santa Cruz #R19, dil 1:4000. Detection Jackson HRP-conj-anti-Go 1:2000. Mo-anti-bFGF  (Upstate #05-118). Dil: 1:2000. Detection HRP-conj-anti-mo 1:2000. Mo-anti-MyoD1 (Novocastra)  dilutions. Dil: 1:500. Detection HRP-conj-anti-mo 1:2000. Difficult to judge size of bands; sizes above 30 not distinguishable Too quick phoresis -wrong gel conc (Zheng-prep)? Separation between 10-20(30) Several small size bands from bFGF. IL-6 still alot of black smearing.  Both bFGF and MyoD seem to work. MyoD only one band of approx correct size. Test decreased conc of anti-goat secondary, 1:4000?
030331 EED LIF rb rerun  LIF rerun mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate. NaAc/Mu 15% Tris-Glycine self-made 1:4000. LIF polyclonal 1:10000 Detection HRP-conj-anti-Rb 1:2000. - All bands visible, except lowermost two bands, are within correct range 38-67 Super: LIF done X3
030401 EED bFGF first run and Zheng retests antibodies IL-6 and MyoD bFGF run mu gastroc, D15,18,11,28 on 25 & 50 µg protein lysate. For IL-6 retest: try more diluted secondary and blocking + secondary using combination block milk +BSA. Note: due to confusion a mix of secondary anti-mo/go was used for MyoD and IL-6. NaAc/Mu 15% Tris-Glycine self-made Mo-anti-bFGF  (Upstate #05-118). Dil: 1:2000. Detection HRP-conj-anti-mo 1:2000. 
Goat-anti-IL-6 Santa Cruz #R19, dil 1:4000. Detection Jackson HRP-conj-anti-Go 1:4000
Mo-anti-MyoD1 (Novocastra)  dilutions. Dil: 1:500. Detection HRP-conj-anti-mo 1:2000. 
bFGF: Specific bands strong signal but some bands of incorrect size.
IL-6 and MyoD1 almost identical spread of multiple bands and high background.
- Secondary Ab anti goat is the problem: background + unspecific bands!
030401 EED bFGF rerun - NaAc/Mu 15% Tris-Glycine self-made - Confirms previous result - -
030403 Zheng Test: MyoD1 and secondaries anti-mo, anti-rb Test: MyoD and secondary antibodies (Amersham) anti-mo, anti-rb 1:2000 (1.5h) after overnight incubation with 5%BSA in PBS but no primary. Test protein: wistar rat lysate NaAc/Mu 15% Tris-Glycine self-made Mo-anti-MyoD1 (Novocastra)  dilutions. Dil: 1:500. Detection HRP-conj-anti-mo 1:2000. 
Secondary test:
HRP-conj-anti-mo 1:2000. HRP-conj-anti-rb 1:2000.
- - -
030701-03 MAL/EED Test of Antibodies: 
P-Akt, Akt, P-Shc, Shc
Mu exctracted with Tris-buffer and protease inhibitor. 50, 100 & 200µg lysate. For Akt Positive and negative controls were used (Cellsignaling #9273) and Positive control for Shc (Upstate #12-301)
Block 1h (PBS + 5%milk + 0.1% Tween20)
Primary overnight (PBS + 5%BSA + 0.1% Tween20)
Secondary 1h (PBS + 5%milk + 0.1% Tween20)
TRIS-(p)/Mu 10% Tris-Glycine self-made Primary Antibodies:
Rb-anti-Shc (Upstate #06-203) 1:000
Rb-anti-P-Shc (Tyr317) (Cellsignaling #2431) 1:1000
Rb-anti-Akt (Cell Signaling #9272) 1:1000
Rb-anti-P-Akt (Ser473) (Cell Signaling #9271) 1:1000
Secondary Antibody:
HRP-conj-anti-Rb 1:2000 for all
Shc, Akt and P-Akt seemd to work, P-Shc did not produce any bands - -
031006 EED Retesting MyoD & IGF-I (mo) Test protein: wistar rat lysate and  positive control for Shc (10µ) (Upstate #12-301). Negative control =primary omitted.
Protocol: 35min 5% milk block, Wx3, Prim 1h; Wx3, Sec 1h, Wx3.
ECL plus used first time. ca 5ml is sufficient to cover membrane (5min incub.).
NaAc/Mu 15% Tris-Glycine self-made Mo-anti-MyoD1 (Novocastra)  dilutions. Dil: 1:500. Detection HRP-conj-anti-mo 1:1000.
Mo-anti-IGF-1 Upstate #05-172. dil: 1:1000. Detection HRP-conj-anti-Mo 1:1000 
Neg control reveals bands very similar to both IGF-I and MyoD1.  Next trial: Dilute secondary more. Try tween-20 instead of Triton-X100 in buffers. Increase myoD1 conc (rec IHC dil =1:80). ECL plus -easy to use, good signal.
031007 EED Retesting MyoD & IGF-I (mo) Test protein: wistar rat lysate. Negative control =primary omitted  NaAc/Mu 15% Tris-Glycine self-made Mo-anti-MyoD1 (Novocastra)  dilutions. Dil: 1:500. Detection HRP-conj-anti-mo 1:2000.
Mo-anti-IGF-1 Upstate #05-172. dil: 1:1000. Detection HRP-conj-anti-Mo 1:2000
Neg control reveals bands very similar to both IGF-I and MyoD1. 
031008 EED Preparing new muscle and liver test/control lysates Preparing new muscle and liver test/control lysates RIPA
NP40, NaDeoxyChol
-
031010 EED Retesting IGF-I (Rb) Test protein: wistar rat lysates, SD liver. Negative control =primary omitted  NaAc/Mu
RIPA/mu/liv
15% Tris-Glycine self-made Mo-anti-IGF-1 Upstate #05-172. dil: 1:1000. Detection HRP-conj-anti-Mo 1:2000