32P labeling of phosphorylated proteins
35S labeling of protein in bacteria
35S labeling of proteins
3D structure database of macromolecules
3'-RACE
5'-RACE
Absorb antibody with acetone protein powder
Acetone protein powder
Adaptation to new media
Agarose gel electrophoresis
Alkaline phosphatase (AP)
Alkaline phosphatase activity secreted
Amino acid structures
Amplification of helper phage
Anesthetizing flies
Animal husbandry
Annealing of oligonucleotides
Antibiotic stocks
Antibody idiotype determination
Antibody storage
Antibody-Protein A or G binding
Antigen retrieval --- autoclave
Antigen retrieval --- microwave
Apoptosis
Asymetric PCR
Autoclave spore test
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
Bac/PAC/cosmid/fosmid prep --- 96 well
Bacteria smear
Bacterial and cell culture waste
Bacterial glycerol stock
Bacterial host strains
Bacterial media
Bacterial plates
Bacterial plates --- X-gal
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
Baculovirus --- virus stock storage
Basic statistics
Beta-gal filter assay
beta-galactosidase (lacZ)
beta-galactosidase acitivity assay --- 96-well
Bioinformatics (51)
Blast
Blast --- local
Blood
Blood smear
BrdU labeling of S phase cells
Buffer exchange
Buffer exchange --- Desalting column
Buffer exchange --- dialysis tubing
Buffer exchange --- Slide-A-Lyzer Dialysis Cassettes
C. elegance
Calcium chloride competent cell
Capture screen image
Cell Biology
Cell count using Coulter Counter
Cell count using hemocytometer
Cell Cycle (9)
Cells on slides --- adherent cells
Cells on slides --- suspension cells
Centricon spin speed and time
Centrifugation froce conversion
Centrifuge
Chi-square test
Chloramphenicol Acetyl Transferase (CAT)
Chloramphenicol Acetyl Transferase (CAT) Assay
Chromosome spread
Classification of amino acids
Cleaning of mercury spills
Cleavage --- Factor Xa
Cleavage --- thrombin
Cloning by FACS
Cloning by limiting dilution
Cloning (74)
Codes for degenerate nucleotides
Collecting eggs
Common harzardous materials in biology lab
Common lab stock solutions and molar concentration
Common PCR and sequencing primers
Common sources of cloning contaminations
Commonly used agarose gel DNA markers
Comparison of embryonic development stages
Concentrating samples
Concentrating samples --- centricon
Concentrating virus (PEG)
Consensus sequences for protein kinases
Converting to pdf files
Counterstain
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
Coupling to biotin
Coupling to fluorochromes
Culture stocks
Data analysis --- filtration
Data analysis --- merge
Data analysis --- missing data fill-in
Data analysis --- normalization
Decontamination of ethidium bromide solutions
Degenerate sequences --- decoding from protein
Deletion of DNA/RNA --- ethidium bromide staining
DEPC treated RNAse-free solutions
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
Disrupting yeast cells
Dissolving peptides
Distinguishing males from females
DNA concentration measurement
DNA end-labeling
DNA labeling by nick translation (32P)
DNA labeling by nick translation (biotin/digoxigenin)
DNA ligation
DNA ligation (quick ligation)
DNA random labeling with 32P-dCTP
DNA random labeling with Biotin/Digoxigenin
Dos and Unix commands
Drawing chemical structures
Drying of polyacrylamide gels --- membrane
Drying of polyamcriamide gels --- vacuum
Dye migration in agarose and polyacrylamide gels
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
Effective range of separation of proteins in PAGE
Electroporation --- parameters for different cells
Electroporation --- recycle cuvettes
ELISA --- alkaline phosphatase detection
ELISA --- horseradish peroxidase detection
ELISA plates
Enhanced Green Fluorescent Protein --- Living Colors
Epitope tags
EST assembler
Establish clean cultures from dechorionated eggs
Establish stable cell clones
Establish stable cell clones --- 96-well
Establish stable cell clones --- cloning cyclinders
Establish stable cell clones --- drug concentrations
Estimation of antibody concentration
Ethanol precipitation of DNA probes
Ethonal precipitation of nucleotic acids
Evolutionary trees
Expression of protein in bacterial cells
Extinction coefficient for oligonucleotide and protein
Extraction of low MW DNA fragments
FASTA format
FCAS analysis
Fixation solutions
Fluorescein labeling of proteins (antibodies) (I)
Fluorescein labeling of proteins (antibodies) (II)
Fly resources
Fly traps
Fly (17)
Food recipe from Bloomington stock center
Formaldehyde/paraformaldehyde/formalin
Formaldehyde-Agarose gels
Freezing cells
Freezing virus
GenBank identifier syntax
Gene annotation databases
Gene nomenclature guidelines
Genetic code --- human mitochondria
Genetic code --- universal
Genetic nomenclature for Drosophila melanogaster
Genetic nomenclature for yeasts
Genome sizes and number of genes
Giemsa stain
Gram stain
Growing bacterial cells --- 96-well
Heat inactivation of serum
Hidden Markov Model --- search for remote relatives
High throughput drug screen (9)
Histology (15)
Histone kinase activity assay
HIV reverse transcriptase activity assay
Homogenizers
Horseradish peroxidase (HRP)
How to calculate IC50
How to tell male from female
HTML
HTML forms
Human disease gene database
Hybridization
Hybridization oven
Hydrophilicity index of amino acids
IC/ED/GI/LD
Immunoprecipitation
In vitro transcription
In vitro transcription/translation --- TNT
In vitro translation
In vitro translation --- Rabbit Reticulocyte Lysate
Incoporation efficiency --- filter binding assay
Incoporation efficiency --- TCA precipiation
Install and run Java
Instant Fly Food
Intensifying screen
Iodination
Iodination --- IODO-BEADS
Isolation of genomic DNA from mouse tails
Isotopes used in biological sciences
Java JAR applications
Kozak translation initiation sequence
Lab equipments (16)
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 of probes
Labeling of proteins
Labeling of samples
Labeling PCR products with Biotin/Digoxigenin
Laminar flow hoods and chemical fume hood
Library Dna
Linear regression
Liquid scintillation counter
Liquid Scintillation Counter efficiency
Liquid Scintillation Counting
Liquid sporulation
Loading buffers
Luciferase activity assay
Luciferase activity assay --- 96-well
Lyophilization --- freeze-dry
Mail DNA/Clone/Stock samples
Male and female symbols
Mass spectrometry
Mating
Measure cell proliferation --- 3H-labeled thymidine
Measure cell proliferation --- BrdU ELISA
Measure cell proliferation --- sulforhodamine B
Measure cell proliferation --- tetrazolium
Measure cell proliferation --- XTT
Metabolic labeling of proteins
Metabolic pathway database
Microarray --- Hierarchical clustering
Microarray --- Tree view
Microarray Explorer
Microarray platforms
Microarray (13)
Microcon cutoff
Miscellaneous (13)
MOI/pfu/TCID50
Molecular weight for amino acids
Molecular weight for oligonucleotide and protein
Mounting medium
Mounting medium --- anti-fade
Mouse diet --- NIH open formula
Mouse ear punch numbering system
Mouse resources
Mouse (12)
Mouse/Rat diet suppliers
Mouth Buccal swab
MSDS (Material Safety Data Sheet)
Multiple sequence alignments
Mutagen Ames test
Mutagen Ames test --- automation
Mycoplasma cure
Mycoplasma test --- PCR
Mycoplasma test --- visulization of DNA
NCI/NIH drug screen program
Normal distribution
Northern
Nucleoside and nucleotide structures
Oligo melting and PCR annealing temperature
Oligonucleotide mole/weight/concentration calculations
ONPG beta-galactosidase activity assay
ORF finder and gene finder
Outliers
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)
Paraffin embedding
Patch grids for 100 mm plates
Pcik a single clone
PCR
PCR --- DpnI-mediated mutagenesis
PCR --- long products
PCR amplification of cDNA library inserts
PCR amplification of library insert
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
PCR (17)
Peptide and phosphodiester bond
Peptide antibody design
Peptide substrates for kinases
Periodic table of the elements
pH indicators
pH meter
pH paper
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
Phalloidin staining of filamentous actin
Phalloidin staining of filamentous actin
Phosphate buffer chart
pK values of amino acids
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
Polyadenylation signal
Polyadnylation --- Ambion PolyA tailing
Preparation of poly-L-lysine-coated slides
Prepare host cells for infection
Prepare paraformaldehyde fix buffer
Prepare slides for printing
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
Promoter sequences
Protease inhibitors
Proteases
Proteasome overlay
Protein concentration --- Bradford (I)
Protein concentration --- Bradford (II)
Protein concentration --- estimate by staining
Protein concentration --- Lowry
Protein concentration --- Modified Lowry
Protein concentration --- UV
Protein dephosphorylation
Protein expression (20)
Protein localization signals
Protein precipitation --- acetone
Protein precipitation --- ethanol
Protein precipitation --- TCA
Protein purification for micro-sequencing --- PVDV
Protein refolding
Protein secondary structure prediction
Protein (32)
PubMed
Purification
Purification --- affinity (I)
Purification --- affinity HiTrap (II)
Purification --- ammonium sulphate precipitation
Purification --- chicken IgY
Purification --- PAGE
Purification --- phospho-antibody
Purification --- protein A column
Purification --- protein G column
Purification --- Sephadex column
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
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
Quantitate kinase activity --- cellulose phosphate filter
Quarantine
Quick freezing of cells on plates or flasks
Radiation protection
Radioactive waste
Recipes
Recipes (1)
Replicate clones in 96 well plates (I)
Replicate clones in 96 well plates (II)
Report genes (6)
Restriction digestion
Reverse transcription
Ribosomal RNA sizes
RNA prep --- phenol (I)
RNA prep --- phenol (II)
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
RNA (19)
RNAse protection
Routes of injection in mouse
RT-PCR --- one-step
Safety and Waste (10)
Salmon sperm DNA
Sample labeling
Screen of recombinant protein expression
Screening for insertion --- blue-white (lacZ)
Screening for insertion --- plasmid size (I)
Screening for insertion --- plasmid size (II)
Sectioning --- frozen tissue
Sectioning --- paraffin block
Sequencing --- ABI Big Dye Terminator
Sequencing --- Dideoxy Chain Termination
Sequencing of GC-rich DNA
Sequencing of PCR products
Sequencing troubleshooting
Serum starvation
Sex of mouse embryo and cell line
Shading of multiple sequence alignments
Shakers
Signal transduction (3)
Single-fly DNA prep for PCR
Single-letter amino acid codes
siRNA design
SNP database
Soft agar assay of colony formation
Software and data mining
Southern --- Chemiluminescence detection
Southern --- radioactive probe
Southern --- stripping
Southern transfer
Spectrometer
Spheroplast
Splicing signal
Stab culture
Stab stocks
Staining --- ABC (DAB)
Staining --- cells on slide
Staining --- formalin-fixed section
Staining --- frozen section
Staining --- membrane
Staining for immunohistochemistry or FACS
Staining of mouse embryo --- AP
Staining of mouse embryo --- lacZ
Staining of proteins
Staining of proteins --- Coomassie blue
Staining of proteins --- quick Coomassie blue
Staining of proteins --- silver
Staining of proteins ---SYPRO
Statistics software
Statistics (7)
Sterilization techniques
Sterilization techniques
Storage freezer
Streaking
Student t-test
Sub-culture of adherent cells
Sub-culture of suspension 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
T3/T7/SP6 minimum promotor sequences
Terminal deoxynucleotidyl transferase
TE-saturated Phenol
Thawing frozen cells
The fruit fly life cycle
The mouse life cycle
Tissue culture waste
Tissue fixation --- ethanol
Tissue fixation --- formalin
Transfection --- Calcium phosphate
Transfection --- electroporation
Transfection --- liposomal
Transfection --- non-liposomal
Transfection --- suspension cells
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
Transformation --- electroporation competent cells
Transformation --- LiAc (I)
Transformation --- LiAc (II)
Transformation --- spheroplast
Translation
Trypsin/EDTA
TUNEL
TUNEL --- FACS
UniGene --- non-redundant gene clusters
Units
UV protection
Vacuum
VecScreen --- vector sequence contamination
Vector for TA cloning
Viewing postscript files
Virgins
Visualization of DNA --- DAPI
Visualization of DNA --- dye list
Visualization of DNA --- Hoechst
Visulization of 3D structures
Visulization of 3D structures on Mac
Water
Water bath
Web restriction digestion
Weight-mole conversion for DNA and protein
Western --- dot blot
Western --- ECL
Western --- stripping
Western transfer
Wet mount
Wipe test for beta emitting radioisotopes
Worm protocols
X-gal staining
X-gal staining of cells
Yeast glycerol stocks
Yeast media
Yeast paste
Yeast resources
Please Cite GEB:
Zhang et al (2010) Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization. BMC Bioinformatics 11: 433
About Arabidopsis GEB
Gene Expression Browser (GEB) is a free online service for scientists to find gene expression profiles. The first version of GEB is delivered with 436 Affymetrix ATH1 Arabidopsis microarray experiments, in which there are 2,007 T/Cs (treatment over control) and 45,460,330 pairs of log2 ratios and P values. The microarray raw data and sample annotation were collected from NASC's Affymetrix Service and NCBI GEO. Users can obtain gene expression profiles by searching the key words in gene annotation, T/C description or experiment description.
Terminology
T/C stands for treatment over control. A T/C is defined with one-factor difference between treatment and control. Meanwhile, the single different factor between treatment and control has clear biological meaning. Therefore, a T/C can be understood as an experimental condition or a single stimulus. GEB T/C View shows the expression change (log2 ratio) of all genes under the T/C condition. Click here to view an example T/C View of "16 hr Pseudomonas infection". Co-regulation T/Cs are a set of T/Cs that have similar expression profiles. Click here to see the co-regulation T/Cs of "16 hr Pseudomonas infection". GEB Gene View shows all T/Cs that affect the expression (log2 ratio) of a selected gene. Click here to visit an example Gene View of Arabidopsis PR-1 gene. Co-responsive genes are a set of genes that simulatively response to different T/Cs. Click here to see the co-responsive genes of PR-1. Both T/C View and Gene View are presented by MA plot. MA plot is used to visualize intensity-dependent ratio of microarray data. The MA plot uses M (log2 ratio of treatment over control) as the y-axis and A (average log2 intensity of treatment and control) as the x-axis. The plot uses data point color code to show the t-test P value of log2 ratio. Blue, green and yellow represents P values of less than 0.01, 0.01-0.05 or larger than 0.05, respectively. Therefore, GEB MA plot displays both the scale and the reliability of ratio data.
Quick Start
Enter key words such as heat, cold or infection into the search box and click Submit to find search results. Click on the link to reach gene expression profile shown by Gene View or T/C View. Use the mouse to drag-and-drop the red square on the top-left MA plot onto the data points to find detailed information of each data point. Click 'select' link to mark the data point on the MA plot. Please have a training by clicking Flash video show, Quick Start, slide show or video show in Youtube (watch in high quality)
License
GEB is composed of a set of software tools, such as data extraction tool, microarray data management system, data annotation tool, data processing pipeline and data search & visualization tool. We can release licenses and provide technical supports to deploy GEB in enterprise's intranet when industrial research institutions have the interests to use GEB for visualizing all thier private gene expression data as totality.
Reference
Zhang et al (2010) Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization. BMC Bioinformatics 11: 433