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The Electronic Protocol Book --- A Quick and Practical Guide for Biologists

Antibody (37)

Absorb antibody with acetone protein powder Antibody idiotype determination
Antibody storage Antibody-Protein A or G binding
Coupling of antibody to biotin Coupling of antibody to protein A or G beads
Coupling of GST-protein to glutathione beads Coupling of peptides for antibody production
Coupling of peptides to Sepharose beads Dissolving peptides
ELISA --- alkaline phosphatase detection ELISA --- horseradish peroxidase detection
ELISA plates Estimation of antibody concentration
Fluorescein labeling of proteins (antibodies) (I) Fluorescein labeling of proteins (antibodies) (II)
Immunoprecipitation Peptide antibody design
Prepare paraformaldehyde fix buffer Production schedule --- monoclonal antibody
Production schedule --- polyclonal in chicken Production schedule --- polyclonal in goat and sheep
Production schedule --- polyclonal in rabbit Production schedule --- polyclonal in rodent
Purification --- affinity (I) Purification --- affinity HiTrap (II)
Purification --- ammonium sulphate precipitation Purification --- chicken IgY
Purification --- phospho-antibody Purification --- protein A column
Purification --- protein G column Staining --- ABC (DAB)
Staining --- cells on slide Staining --- formalin-fixed section
Staining --- frozen section Staining --- membrane
Staining for immunohistochemistry or FACS

Apoptosis (3)

Extraction of low MW DNA fragments TUNEL
TUNEL --- FACS

Appendix (41)

Amino acid structures Centricon spin speed and time
Centrifugation froce conversion Classification of amino acids
Codes for degenerate nucleotides Common lab stock solutions and molar concentration
Common PCR and sequencing primers Commonly used agarose gel DNA markers
Comparison of embryonic development stages Consensus sequences for protein kinases
Dye migration in agarose and polyacrylamide gels Extinction coefficient for oligonucleotide and protein
Gene nomenclature guidelines Genetic code --- human mitochondria
Genetic code --- universal Genome sizes and number of genes
Hydrophilicity index of amino acids Kozak translation initiation sequence
Loading buffers Mail DNA/Clone/Stock samples
Male and female symbols Microcon cutoff
Molecular weight for amino acids Molecular weight for oligonucleotide and protein
Nucleoside and nucleotide structures Oligo melting and PCR annealing temperature
Peptide and phosphodiester bond Periodic table of the elements
pH indicators Phosphate buffer chart
pK values of amino acids Polyadenylation signal
Promoter sequences Protease inhibitors
Proteases Protein localization signals
Single-letter amino acid codes Splicing signal
T3/T7/SP6 minimum promotor sequences Units
Weight-mole conversion for DNA and protein

Bioinformatics (51)

3D structure database of macromolecules Automation --- automatic archiving old files
Automation --- Microsoft Excel macros Automation --- Microsoft Excel tables
Automation on Mac --- AppleScript Automation on Mac --- iDo Script Scheduler
Automation on PC --- batch files Automation on PC --- scheduled task
Blast Blast --- local
Capture screen image Converting to pdf files
Drawing chemical structures Dos and Unix commands
EST assembler Evolutionary trees
FASTA format GenBank identifier syntax
Gene annotation databases Hidden Markov Model --- search for remote relatives
HTML HTML forms
Human disease gene database Install and run Java
Java JAR applications Mass spectrometry
Metabolic pathway database Multiple sequence alignments
ORF finder and gene finder Perl
Perl Example 1 --- file preview Perl Example 2 --- remove digits and spaces
Perl Example 3 --- insert links Perl Example 4 --- count frequency
Perl Example 5 --- data merge Perl Example 6 --- archive old files
Perl On Mac Perl On Mac --- MacPerl
Perl On Windows Pfam --- database of protein domains
Protein secondary structure prediction PubMed
Shading of multiple sequence alignments SNP database
Translation UniGene --- non-redundant gene clusters
VecScreen --- vector sequence contamination Viewing postscript files
Visulization of 3D structures Visulization of 3D structures on Mac
Web restriction digestion

C. elegance (1)

Worm protocols

Cell Biology (45)

Alkaline phosphatase activity --- secreted Adaptation to new media
beta-galactosidase acitivity assay --- 96-well Cell count using Coulter Counter
Cell count using hemocytometer Cells on slides --- adherent cells
Cells on slides --- suspension cells Chloramphenicol Acetyl Transferase (CAT) Assay
Chromosome spread Cloning by FACS
Cloning by limiting dilution Epitope tags
Establish stable cell clones Establish stable cell clones --- 96-well
Establish stable cell clones --- cloning cyclinders Establish stable cell clones --- drug concentrations
Freezing cells Heat inactivation of serum
Luciferase activity assay --- 96-well Metabolic labeling of proteins
MOI/pfu/TCID50 Mycoplasma cure
Mycoplasma test --- PCR Mycoplasma test --- visulization of DNA
ONPG beta-galactosidase activity assay Phalloidin staining of filamentous actin
Preparation of poly-L-lysine-coated slides Quick freezing of cells on plates or flasks
Serum starvation Soft agar assay of colony formation
Sterilization techniques Sub-culture of adherent cells
Sub-culture of suspension cells Thawing frozen cells
Tissue culture waste Transfection --- Calcium phosphate
Transfection --- electroporation Transfection --- liposomal
Transfection --- non-liposomal Transfection --- suspension cells
Trypsin/EDTA Visualization of DNA --- DAPI
Visualization of DNA --- dye list Visualization of DNA --- Hoechst
X-gal staining of cells

Cell Cycle (9)

BrdU labeling of S phase cells FCAS analysis
Histone kinase activity assay Synchronization of cells --- double thymidine block
Synchronization of cells --- growth condition Synchronization of cells --- mitotic shake-off
Synchronization of cells --- nocodazole Synchronization of cells --- summary
Synchronization of cells --- yeast alpha-factor

Cloning (74)

3'-RACE 5'-RACE
Agarose gel electrophoresis Annealing of oligonucleotides
Antibiotic stocks Bacterial glycerol stock
Bacterial host strains Bacterial media
Bacterial plates Bacterial plates --- X-gal
Calcium chloride competent cell Common sources of cloning contaminations
Deletion of DNA/RNA --- ethidium bromide staining Dephosphorylation of DNA --- CIP
Dephosphorylation of DNA --- SAP Detection of DNA --- fluorometer (Hoechst )
Detection of DNA --- fluorometer (Pico green) Detection of DNA/RNA --- methylene blue staining
Detection of DNA/RNA --- spectrometer Detection of DNA/RNA --- SYBR Green staining
Detetion of DNA --- colorimetric Detetion of DNA in PAGE --- UV shadowing
DNA concentration measurement DNA ligation
DNA ligation (quick ligation) Effective range of separation of DNAs in agarose gels
Effective range of separation of DNAs in PAGE Effective range of separation of DNAs in PAGE/Urea
Ethonal precipitation of nucleotic acids Growing bacterial cells --- 96-well
Patch grids for 100 mm plates Pcik a single clone
Plasmid miniprep --- alkaline lysis Plasmid miniprep --- boiling
Plasmid prep --- 96-well Plasmid prep --- CsCl
Plasmid prep --- Midi/Maxi column (Qiagen) Plasmid prep --- Qiagen mini
Polyacriamide gels Polyacriamide/urea gels
Purification of DNA from agarose gels --- DEAE cellulose Purification of DNA from agarose gels --- Qiagen column
Purification of DNA from agarose gels --- silica beads Purification of DNA from PAGE gels
Replicate clones in 96 well plates (I) Replicate clones in 96 well plates (II)
Restriction digestion Salmon sperm DNA
Screening for insertion --- blue-white (lacZ) Screening for insertion --- plasmid size (I)
Screening for insertion --- plasmid size (II) Sequencing --- ABI Big Dye Terminator
Sequencing --- Dideoxy Chain Termination Sequencing of GC-rich DNA
Sequencing troubleshooting Southern --- Chemiluminescence detection
Southern --- radioactive probe Southern --- stripping
Southern transfer Stab culture
Stab stocks Sterilization techniques
Streaking Terminal deoxynucleotidyl transferase
TE-saturated Phenol Transfer of nucleotic acids to membrane --- capillary
Transfer of nucleotic acids to membrane --- large fragment Transfer of nucleotic acids to membrane --- PAGE
Transfer of nucleotic acids to membrane --- vacuum Transformation
Transformation --- competent cells Transformation --- electroporation
Transformation --- electroporation competent cells Vector for TA cloning

Fly (17)

Anesthetizing flies Collecting eggs
Culture stocks Distinguishing males from females
Establish clean cultures from dechorionated eggs Fly resources
Fly traps Food recipe from Bloomington stock center
Genetic nomenclature for Drosophila melanogaster Instant Fly Food
Mating Quarantine
Single-fly DNA prep for PCR The fruit fly life cycle
Virgins X-gal staining
Yeast paste

High throughput drug screen (9)

HIV reverse transcriptase activity assay How to calculate IC50
IC/ED/GI/LD Measure cell proliferation --- 3H-labeled thymidine
Measure cell proliferation --- BrdU ELISA Measure cell proliferation --- sulforhodamine B
Measure cell proliferation --- tetrazolium Measure cell proliferation --- XTT
NCI/NIH drug screen program

Histology (15)

Antigen retrieval --- autoclave Antigen retrieval --- microwave
Blood smear Counterstain
Fixation solutions Formaldehyde/paraformaldehyde/formalin
Giemsa stain Gram stain
Mounting medium Mounting medium --- anti-fade
Paraffin embedding Sectioning --- frozen tissue
Sectioning --- paraffin block Tissue fixation --- ethanol
Tissue fixation --- formalin

Lab equipments (16)

Autoclave spore test Centrifuge
Electroporation --- parameters for different cells Electroporation --- recycle cuvettes
Homogenizers Hybridization oven
Laminar flow hoods and chemical fume hood pH meter
pH paper Shakers
Spectrometer Storage freezer
Vacuum Water
Water bath Liquid scintillation counter

Labeling of probes (21)

DNA end-labeling DNA labeling by nick translation (32P)
DNA labeling by nick translation (biotin/digoxigenin) DNA random labeling with 32P-dCTP
DNA random labeling with Biotin/Digoxigenin Ethanol precipitation of DNA probes
Incoporation efficiency --- filter binding assay Incoporation efficiency --- TCA precipiation
Intensifying screen Isotopes used in biological sciences
Labeling of cDNA --- Amino-allyl dye coupling Labeling of cDNA --- Cy3/Cy5 direct
Labeling of DNA --- Amino-allyl dye coupling Labeling of DNA in agarose gel
Labeling PCR products with Biotin/Digoxigenin Liquid Scintillation Counter efficiency
Liquid Scintillation Counting Oligonucleotide mole/weight/concentration calculations
Purification Purification --- PAGE
Purification --- Sephadex column

Labeling of proteins (8)

32P labeling of phosphorylated proteins 35S labeling of protein in bacteria
35S labeling of proteins Coupling to biotin
Coupling to fluorochromes In vitro translation
Iodination Iodination --- IODO-BEADS

Library (10)

Amplification of helper phage Bac/PAC/cosmid/fosmid prep --- 96 well
PCR amplification of library insert Phage clone --- pick clones for storage
Phage clone --- storage Phage DNA prep --- lambda phage
Phage library --- tittering Phage library screening --- PCR (I)
Phage library screening --- Southern Prepare host cells for infection

Microarray (13)

Data analysis --- filtration Data analysis --- merge
Data analysis --- missing data fill-in Data analysis --- normalization
Hybridization Labeling of samples
Microarray --- Hierarchical clustering Microarray --- Tree view
Microarray Explorer Microarray platforms
Sample labeling Software and data mining
Prepare slides for printing

Miscellaneous (13)

Bacteria smear Buffer exchange
Buffer exchange --- Desalting column Buffer exchange --- dialysis tubing
Buffer exchange --- Slide-A-Lyzer Dialysis Cassettes Concentrating samples
Concentrating samples --- centricon Lyophilization --- freeze-dry
Mouth Buccal swab Mutagen Ames test
Mutagen Ames test --- automation Proteasome overlay
Wet mount

Mouse (12)

Animal husbandry How to tell male from female
Isolation of genomic DNA from mouse tails Mouse diet --- NIH open formula
Mouse ear punch numbering system Mouse resources
Mouse/Rat diet suppliers Routes of injection in mouse
Sex of mouse embryo and cell line Staining of mouse embryo --- AP
Staining of mouse embryo --- lacZ The mouse life cycle

PCR (17)

Asymetric PCR PCR
PCR --- DpnI-mediated mutagenesis PCR --- long products
PCR amplification of cDNA library inserts PCR amplification of single clones
PCR amplification of yeast clones PCR cleanup --- 96-well
PCR cleanup --- agarose gel PCR cleanup --- Microcon
PCR cleanup --- Qiaquick spin column PCR cleanup --- SAP/ExoI
PCR construction of insertion/deletion/mutation/fusion PCR from blood smears
PCR primer design PCR random mutagenesis
Sequencing of PCR products

Protein (32)

Acetone protein powder Degenerate sequences --- decoding from protein
Drying of polyacrylamide gels --- membrane Drying of polyamcriamide gels --- vacuum
Effective range of separation of proteins in PAGE In vitro transcription/translation --- TNT
In vitro translation --- Rabbit Reticulocyte Lysate PAGE --- gel casting
PAGE/Native PAGE/Native --- recipe calculator (30% stock)
PAGE/Native --- recipe calculator (40% stock) PAGE/SDS --- recipe calculator (30% stock)
PAGE/SDS --- recipe calculator (40% stock) Protein concentration --- Bradford (I)
Protein concentration --- Bradford (II) Protein concentration --- estimate by staining
Protein concentration --- Lowry Protein concentration --- Modified Lowry
Protein concentration --- UV Protein precipitation --- acetone
Protein precipitation --- ethanol Protein precipitation --- TCA
Protein purification for micro-sequencing --- PVDV Staining of proteins
Staining of proteins --- Coomassie blue Staining of proteins --- quick Coomassie blue
Staining of proteins --- silver Staining of proteins ---SYPRO
Western --- dot blot Western --- ECL
Western --- stripping Western transfer

Protein expression (20)

Baculovirus --- virus stock storage Baculovirus --- amplifying virus stock
Baculovirus --- cluturing of insect cells Baculovirus --- freezing and thawing of insect cells
Baculovirus --- infection Baculovirus --- plaque assay
Baculovirus --- plaque purification of virus stock Cleavage --- Factor Xa
Cleavage --- thrombin Concentrating virus (PEG)
Expression of protein in bacterial cells Freezing virus
Protein refolding Purification of GST-fusion protein
Purification of his-tagged protein --- HiTrap Purification of his-tagged protein --- TALON
Purification of inclusion body proteins Purification of inclusion body proteins --- HiTrap
Purification of moltose-binding protein fusion Screen of recombinant protein expression

Recipes (1)

Recipes

Report genes (6)

Alkaline phosphatase (AP) beta-galactosidase (lacZ)
Chloramphenicol Acetyl Transferase (CAT) Enhanced Green Fluorescent Protein --- Living Colors
Horseradish peroxidase (HRP) Luciferase activity assay

RNA (19)

DEPC treated RNAse-free solutions Formaldehyde-Agarose gels
In vitro transcription Northern
Polyadnylation --- Ambion PolyA tailing Reverse transcription
Ribosomal RNA sizes RNA purification --- acid phenol:chloroform extraction
RNA purification --- DNase I digestion RNA purification --- guanidinium thiocyanate
RNA purification --- hot phenol RNA purification --- LiCl precipitation
RNA purification --- polyA (I) RNA purification --- polyA (II)
RNA purification --- Qiagen Rneasy RNA purification --- Trizol
RNAse protection RT-PCR --- one-step
siRNA design

Safety and Waste (10)

Bacterial and cell culture waste Blood
Cleaning of mercury spills Common harzardous materials in biology lab
Decontamination of ethidium bromide solutions MSDS (Material Safety Data Sheet)
Radiation protection Radioactive waste
UV protection Wipe test for beta emitting radioisotopes

Signal transduction (3)

Peptide substrates for kinases Protein dephosphorylation
Quantitate kinase activity --- cellulose phosphate filter

Statistics (7)

Basic statistics Chi-square test
Linear regression Normal distribution
Outliers Statistics software
Student t-test

Yeast (15)

Beta-gal filter assay Disrupting yeast cells
Genetic nomenclature for yeasts Liquid sporulation
Phalloidin staining of filamentous actin RNA prep --- phenol (I)
RNA prep --- phenol (II) Spheroplast
Transformation --- electroporation Transformation --- LiAc (I)
Transformation --- LiAc (II) Transformation --- spheroplast
Yeast glycerol stocks Yeast media
Yeast resources
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