Production of gelatinase

RNA isolation

DTH

GFP-β-catenin- C (634 -781 a.a)

10 mM Tris-HCl (pH 8.0)1 mM EDTA Tris-Acetic acid EDTA (TAE) buffer:40 mM Tris base 0.5 M EDTApH was adjusted to 8.5 with glacial acetic acid.This was prepared as a 50 X stock solution and used at a 1 X concentration. Tris-Borate EDTA (TBE) buffer:90 mM Tris-borate 2 mM EDTA (pH 8.0) pH was adjusted to 8.3withHCl.This was prepared as a 10 X stock solution and used at a 1 X concentration.Both TAE and TBE were used asstandard gel electrophoresis buffers.HEPES buffer:This was used to prepare YNB medium of different pH.1M HEPESpH was adjusted to 7.5withNaOH.Bufferwas filter-sterilized and stored in an amber-coloured bottle. Citrate buffer(0.1M, pH 5.5):4.7 volume of 0.1 M Citric acid 15.4 volume of 0.1 M Sodium citrate

Phosphate-Buffered Saline (PBS):137 mM NaCl 2.7 mM KCl10 mM Na2HPO42 mM KH2PO4pH was adjusted to 7.3.This was prepared as a 10 X stock solution andused at a 1 X concentration.Tris-HCl buffer:0.5 M TrizmaBase pH was adjusted to7.6 using concentrated HCl.This was prepared as a 10 X stock solution andused at a 1 X concentration.Tris-EDTA (TE)buffer:

Common buffers

Fixative : 4% Formaldehyde

Ethylene Glycol Tetraacetic acid (EGTA), pH 7.0ComponentsFinal concentrationFor 50 mlEGTA0.1M1.902gH2Oq.sThe pH is adjusted to 7.0 using 10M NaOH

Extraction buffer

MTT reagent

For Cytotoxicity assays

6XEMSA sample loading dye

5X EMSA buffer

Native EMSA PAGE

10XBinding buffer

For Electrophoretic Mobility Shift Assay (EMSA)

For preparation of Ultra competent cells

Inoue buffer

6X DNA loading dye

Agarose gel

TAE

For DNA electrophoresis

Nuclear lysis buffer (without protease inhibitors

Cytoplasmic extraction buffer (without protease inhibitors)

For Cell fractionation

Blocking buffer: 2% BSA

Permeabilisation buffer: 0.2% Triton X100

4% Formaldehyde fixative

For Immunofluorescence(IF)

Stripping buffer

Blocking buffer

TBS-T

Transfer buffer

(f) Running buffer

(e) Stacking polyacrylamide gel

(d) Resolvingpolyacrylamide gel

(c) 6X Protein loading buffer (Lammeli buffer)

(b) Celllysis buffer B(For IB)

Cell lysis bufferA(For IP)

II. For Immunoprecipitation(IP)and Immunoblotting(IB)

Table 2.1: Commonly used buffers and solutionsI. General buffers(a)Phosphate Buffered Saline (PBS)

10 mM Ferric ethylenediaminetetraacetic acid (Fe(III)EDTA)100 mM Magnesium chloride (MgCl2)Working solution 0.18% Xylose 670 μM L-Methionine10 mM Sodium glutamate14.7 mM Potassium dihydrogen phosphate (KH2PO4)40 μM Mangenese sulphate (MnSO4)240 μM Ferric ethylenediaminetetraacetic acid (Fe(III)EDTA)5 mM Magnesium chloride (MgCl2)1.2% AgarLuria Bertani (LB)0.5% Yeast extract1% Tryptone1% Sodium cholride (NaCl)Media and solutions were sterilized either by routine autoclaving at 121°C and 15 psi for 20 min or by filtration through membrane of 0.22 μM porosity

Peptone Sucrose (PS)1 % Peptone1 % SucroseFor preparing plates, 1.2 % agar was added to the medium before autoclaving.Minimal Medium (MM9)Stock SolutionMinimal Salt (2X) for 250 mL 5.25 g di-Potassium hydrogen phosphate (K2HPO4) 2.25 g Potassium dihydrogen phosphate (KH2PO4)0.5 g Ammonium sulphate (NH4)2SO40.25 g Tri-Sodium citrate (Na3citrate)1 M Magnesium sulphate heptahydrate (MgSO4.7H2O) -250 μl 25 mg/mL L-Methionine-1 ml25 mg/mL Nicotinic acid-1 ml10 mg/mL Glutamic acid-25 ml20% Glucose-12.5 ml3% Agar-100 mlPlant mimicking medium (XOM2)Stock preparation100 mM L-Methionine1 M Sodium glutamate1 M Potassium dihydrogen phosphate (KH2PO4)10 mM Manganese sulphate (MnSO4)

Bacterial media