The Electronic Protocol Book---A Quick and Practical Guide for Biologists (original) (raw)
Antibody (37)
Absorb antibody with acetone protein powder
Antibody idiotype determination
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
ELISA --- alkaline phosphatase detection
ELISA --- horseradish peroxidase detection
Estimation of antibody concentration
Fluorescein labeling of proteins (antibodies) (I)
Fluorescein labeling of proteins (antibodies) (II)
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 HiTrap (II)
Purification --- ammonium sulphate precipitation
Purification --- phospho-antibody
Purification --- protein A column
Purification --- protein G column
Staining --- formalin-fixed section
Staining for immunohistochemistry or FACS
Apoptosis (3)
Extraction of low MW DNA fragments
Appendix (41)
Centrifugation froce conversion
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
Genetic code --- human mitochondria
Genome sizes and number of genes
Hydrophilicity index of amino acids
Kozak translation initiation sequence
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
Single-letter amino acid codes
T3/T7/SP6 minimum promotor sequences
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
Hidden Markov Model --- search for remote relatives
Perl Example 1 --- file preview
Perl Example 2 --- remove digits and spaces
Perl Example 3 --- insert links
Perl Example 4 --- count frequency
Perl Example 6 --- archive old files
Pfam --- database of protein domains
Protein secondary structure prediction
Shading of multiple sequence alignments
UniGene --- non-redundant gene clusters
VecScreen --- vector sequence contamination
Visulization of 3D structures on Mac
C. elegance (1)
Cell Biology (45)
Alkaline phosphatase activity --- secreted
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
Establish stable cell clones --- 96-well
Establish stable cell clones --- cloning cyclinders
Establish stable cell clones --- drug concentrations
Luciferase activity assay --- 96-well
Metabolic labeling of proteins
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
Soft agar assay of colony formation
Sub-culture of suspension cells
Transfection --- Calcium phosphate
Transfection --- electroporation
Transfection --- non-liposomal
Transfection --- suspension cells
Visualization of DNA --- dye list
Visualization of DNA --- Hoechst
Cell Cycle (9)
BrdU labeling of S phase cells
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)
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
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
Plasmid miniprep --- alkaline lysis
Plasmid prep --- Midi/Maxi column (Qiagen)
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)
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
Southern --- Chemiluminescence detection
Southern --- radioactive probe
Terminal deoxynucleotidyl transferase
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 --- competent cells
Transformation --- electroporation
Transformation --- electroporation competent cells
Fly (17)
Distinguishing males from females
Establish clean cultures from dechorionated eggs
Food recipe from Bloomington stock center
Genetic nomenclature for Drosophila melanogaster
High throughput drug screen (9)
HIV reverse transcriptase activity assay
Measure cell proliferation --- 3H-labeled thymidine
Measure cell proliferation --- BrdU ELISA
Measure cell proliferation --- sulforhodamine B
Measure cell proliferation --- tetrazolium
Measure cell proliferation --- XTT
Histology (15)
Antigen retrieval --- autoclave
Antigen retrieval --- microwave
Formaldehyde/paraformaldehyde/formalin
Lab equipments (16)
Electroporation --- parameters for different cells
Electroporation --- recycle cuvettes
Laminar flow hoods and chemical fume hood
Labeling of probes (21)
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
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
Oligonucleotide mole/weight/concentration calculations
Purification --- Sephadex column
Labeling of proteins (8)
32P labeling of phosphorylated proteins
35S labeling of protein in bacteria
Library (10)
Bac/PAC/cosmid/fosmid prep --- 96 well
PCR amplification of library insert
Phage clone --- pick clones for storage
Phage DNA prep --- lambda phage
Phage library screening --- PCR (I)
Phage library screening --- Southern
Prepare host cells for infection
Microarray (13)
Data analysis --- missing data fill-in
Data analysis --- normalization
Microarray --- Hierarchical clustering
Miscellaneous (13)
Buffer exchange --- Desalting column
Buffer exchange --- dialysis tubing
Buffer exchange --- Slide-A-Lyzer Dialysis Cassettes
Concentrating samples --- centricon
Mutagen Ames test --- automation
Mouse (12)
Isolation of genomic DNA from mouse tails
Mouse diet --- NIH open formula
Mouse ear punch numbering system
Sex of mouse embryo and cell line
Staining of mouse embryo --- AP
Staining of mouse embryo --- lacZ
PCR (17)
PCR --- DpnI-mediated mutagenesis
PCR amplification of cDNA library inserts
PCR amplification of single clones
PCR amplification of yeast clones
PCR cleanup --- Qiaquick spin column
PCR construction of insertion/deletion/mutation/fusion
Protein (32)
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/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 precipitation --- acetone
Protein precipitation --- ethanol
Protein purification for micro-sequencing --- PVDV
Staining of proteins --- Coomassie blue
Staining of proteins --- quick Coomassie blue
Staining of proteins --- silver
Protein expression (20)
Baculovirus --- virus stock storage
Baculovirus --- amplifying virus stock
Baculovirus --- cluturing of insect cells
Baculovirus --- freezing and thawing of insect cells
Baculovirus --- plaque purification of virus stock
Expression of protein in bacterial cells
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)
Report genes (6)
Chloramphenicol Acetyl Transferase (CAT)
Enhanced Green Fluorescent Protein --- Living Colors
RNA (19)
DEPC treated RNAse-free solutions
Polyadnylation --- Ambion PolyA tailing
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
Safety and Waste (10)
Bacterial and cell culture waste
Common harzardous materials in biology lab
Decontamination of ethidium bromide solutions
MSDS (Material Safety Data Sheet)
Wipe test for beta emitting radioisotopes
Signal transduction (3)
Peptide substrates for kinases
Quantitate kinase activity --- cellulose phosphate filter
Statistics (7)
Yeast (15)
Genetic nomenclature for yeasts
Phalloidin staining of filamentous actin
Transformation --- electroporation