Table of Contents

Analyses for Association of Protein with DNA

ChIP Assay
ChIPping for Dummies
ChIP LM-PCR (by Nimblegen)
Dideoxynucleotide Sequencing
DnaseI Footprinting
Electrophoretic Mobility Shift Assay ver1
Electrophoretic Mobility Shift Assay ver2
Filter Binding Assay

Antibodies

EBNA-1 Ab Purification from Mouse
LMP-1 Antibody Purification

Cell Culture

Picking Cloned Cells
Tissue Culture Stocks
Toxic Dose of Antibiotics for Cell Lines

Immunofluorescent Staining and Fluorescence In Situ Hybridization

FISH ver1
FISH ver2
Immunofluorescent Staining

LMP-1 Study

Immunofluorescent Staining for LMP1
Lipid Raft Flotation Assay
LMP-1 Pulse Chase
NF-KB Reporter Assay

Molecular Cloning

Alkaline Lysis Plasmid Prep ver1
Alkaline Lysis Plasmid Prep ver2
Alkaline Lysis of Bacteria and Maxi Plasmid Prep
Colony PCR Screen for Bacterial Cloning ver1
Colony PCR Screen for Bacterial Cloning ver2
Common Reagents for Bacteria
Common Reagents for Molecular Cloning
DNA Sequencing
Ethanol Precipitation and Phenol-Chloroform Extraction
Ligation and Transformation
Plasmid Shipment
Preparation of Chemical Competent cells and Chemical-Transformation
Preparation of Electrocompetent Cells and Electro-Transformation
Triton X100 Plasmid Prep

Northern Blot/RT-PCR

Fractionation of Nuclear and Cytoplasmic RNA by Trizol
Preparation of Total Cellular RNA
RNA Isolation and cDNA Synthesis from B-cells
Standard Real-time PCR Protocol
Stripping of Blot

Preparation of maxiEBV

CsCl Prep for maxiEBV
Establishing Stable 293/maxiEBV Clones
Induction of Virus Production from Stable Cell Lines Harboring EBV
Isolating Primary B-Cells
Mini Prep for maxiEBV
Recombination and Competent Cells

Protein Expression in E. coli

Purification of 6xHis-tagged proteins by Ni-NTA-Agarose ver1
Purification of 6xHis-tagged proteins by Ni-NTA-Agarose ver2
Purification of dnEBNA-1/Soft-tag from E. coli BL21 LysS (p3134)
Purification of GST-fusion protein in E.coli ver1
Purification of GST-fusion protein in E.coli ver2
Purification of GST-fusion protein in E.coli ver3
Purification of GST-fusion protein in E.coli ver4
Thrombin Cleavage

Replication Study

2-Dimensional Gel
BND-Cellulose Absorption
Measurement of Establishment Efficiency
S1 Nuclease Mapping

SDS-PAGE and Western Blot

Protein Concentration
SDS-PAGE Gels Preparation
SDS-PAGE Recipe 8-15%
Western Blot
Western Blot Analysis

Southern Blot

Alkaline Lysis of Mammalian Cells for Southern Blotting
Classic Hirt Extraction
Gardella Gel
Isolation of Total Cellular DNA
Southern Blotting
*Stripping of Blot protocol is under Northern Blot/RT-PCR above.

Transfection and Retrovirus Infection

96 Well Plate Dual Luciferase Assay
Preparation and Infection of Retrovirus
Titering Virus Stocks
Transfection by DEAE/Chloroquine
Transfection by Lipofectamine
Transfection by Electroporation