Alternate method for purifying DNA from agarose gels
Isolation of RNA from mammalian cells using RNAZOL (Teltest)
Preparation of sequencing gels
Preparing proteins/antibodies/DNA/RNA for microinjection
Safety Procedures
Preparation of Solutions
Disposal of Buffers and Chemicals
Equipment
Transfection of mammalian cells using Lipofectamine (LTI)
Transformation of E. coli by electroporation
Chapter 2. Microscope Technology
Additional Applications of Confocal Microscopy
Comparison of Electron Micrographs
Confocal Microscopy (Information about the history, confocal theory, principles and optics as well as a selection of general links)
Conventional VS Laser scanning Microscopy Techniques
Creatingand enhancing professional graphics using Adobe PhotoshopCS3
Dark field illumination, Larry Legg
Digital Image Ethics (A short history of some of the issues that journalists have struggled with and ten suggested guidelines for working with digital images)
Digital Microscope Camera Technology
Confocal Laser Scanning Microscopy
Light Microscope Techniques
Materials, Forensics, Geological Microscopy
Electron and Light Microscopy Web Resources
Educational Resources (On-line resources for K-12 teachers & students)
Electron Microscope Techniques
Historical and Antique Microscopes
Scanning Probe and Atomic Force
Energy Dispersive Microanalysis EDX
Electron Microscopy (Information about history, principles, sample preparation techniques and www resources for TEM & SEM)
Fluorescence Techniques (Links with information about fluorescent dyes, antibodies and resources for sample preparation)
Free Publications (Seven publications for professionals that cover microscopy & imaging from a variety of perspectives)
Hardware (Information about digital cameras, scanners and printers)
Histology (Links to sample preparation protocols and staining techniques, immuno/histo/cyto-chemistry, collections of images of tissues prepared for histology and safety)
Image Galleries (Links to collections of beautiful images that use a number of microscopic imaging techniques0
Introduction (A look at the basics of what makes up a digital image, color and file formats, as well as a few links on human vision)
Laser microscopy: stereo-viewer
Light & Microscopes Larry Legg's funky introduction
Light Microscopy (Links to excellent resources that introduce concepts of light & optics, as well as how light microscopes work)
McCrone Research Institute Teaching light microscopy, pollen and spore identification
Measurement of Cell Organelles
Measurements: Ocular and Stage Micrometers
Microscopy - Wikipedia, the free encyclopedia
Microscopy Resources (General information about professional societies, vendors, web resources and email discussion groups)
Microscopy-UK general resource, training, and supplies
Phase Contrast illumination and other methods, Larry Legg
Polarized light illumination - Do-it-yourself, cheap
Polarized Light illumination, David Walker
Sample Preparation of Confocal Microscopy
Software (Links to resources for several commercial and freeware image editing programs)
The Transmission Electron Microscope
Video microscopy (Microscopy & Imaging Resources on the WWW)
Chapter 3. Histochemistry Protocols
Alkaline Phosphatase Localization
Cell fixation - room temperature paraformaldehyde (good for paraspeckles/speckles for 5 min; most other things for 10 min)
Cell fixation - methanol
Conjugating antibodies to fluorescent probes
Immunoflourescence of MEFs
Mouse Necropsy
Necropsy form
Paraffin embedding and Sectioning
Staining Protocols
H & E staining
BrdU Staining Histological Sections
X-gal Staining
HRP-DAB Immunostaining
AP-BCIP/NBT Immunostaining
GFP & BrdU In Situ Immunoflourescence
Fixation, permeabilization and immunostaining of cells (contains images and movies)
Cell fixation - warm paraformaldehyde (preserves microtubules)
Immunofluorescent Localization of Tubulin
Methyl Green-Pyronin Staining of DNA and RNA
Periodic Acid Schiff (PAS) Reaction
Chapter 4. Protein
Affinity column preparation and Immunoprecipitation
Affinity purification of Antibodies
B-PER Bacterial Protein extraction reagent (Pierce)
Bradford quantification of protein concentration
Crosslinking the antibody to the beads protocol | Abcam
Factor Xa Cleavage of GST fusions
GST-fusion protein injection into rabbits
GST-protein fusion expression, purification and other uses
His-fusion protein purification (Novagen/Qiagen)
Histone Kinase Assay
Western blot
p27 ELISA
Protein Interactions Captured by Chemical Cross-linking: One-Step Cross Linking.
Protein preparation (from plants tissue)
Protocol: Cross-linking of IgG to Protein A or G Beads: NEB
Cell Fractionation Protocol.
Chromatin isolation
Spliceosome purification
Cell Fractionation Protocol.
Covalently conjugate antibodies to beads for affinity purification
Nucleolar isolation (contains images and movies)
Cajal body isolation (contains images and movies)
Lysing cells for release of both cytoplasmic and nuclear proteins
Equilibrium Density Gradient - Percoll
Preparation of nuclear extract from plated cells
Chapter.7. RNA
Amino-allyl labeling
BioAnalyzer
TRIzol plus RNEasy Mini
RNEasy Midi
TRIzol product insert
RNA amplification
RNA gel electrophoresis
C. elegans RNA prep: Michael Koelle
In vitro transcription reaction
Northern Blots: Michael Koelle
Phenol extraction of rRNA (rat liver)
RNA and protein extraction from the same sample
RNA prepararion (from plants tissue)
RNA Preparation: MGH
Chapter.8. DNA
ABC Random Amplification
Alcohol Precipitation of DNA
AML sample DNA preparation
Boomerang DNA Amplification Single primer DNA amplification
cDNA amplification from l-phage library
DIG DNA labelling and hybrid detection (Boehringer Mannheim)
Direct Automated Sequencing off Bacterial Genomic DNABruce Rhoe
DNA extraction from agarose (Qiagen)
DNA - dische diphenylamine determination
DNA Fragment Isolation from LM agarose
DNA detection
DAPI chromosome identification
DNA preparation by cryostom tissue dissection
DNA labeling by nick translation
Extraction of DNA from bovine spleen
Genomic DNA preparation (plants)
Hybridization
Large Scale Plasmid Preparation: MGH
PCR product purification (Qiagen)
Perfectly Blunt Cloning of DNA (Novagen)
Phenol/chloroform extraction of DNA
Plasmid midi-prep from bacteria
Preparation of genomic DNA from bacteria
Random Primed labeling of DNA (Prime-It II -Stratagene)
Restriction enzyme digestion of DNA
Southern Hybridization
Stark's Prehybridization Buffer
Wizard Plus Mini-preps (109. Plasmid Mini-prep)
Worm genomic Southern blots: Michael Koelle
Chapter.9. PCR
Competitive and/or Quantitative RT-PCR
History of Polymerase chain reaction (PCR)--(1)
History of Polymerase chain reaction (PCR)--(2)
Important Publications at Cell
Important Publications at Nature
Important Publications at Science
Ligation Mediated Suppression PCR
Long PCR Protocol: Church Lab
PCR, RT-PCR, and Real Time PCR Tutorials
Polymerase Chain Reaction (Molecular Info)
Polymerase chain reaction--PCR
PCR Web Source (from Google directory)
A Rapid DNA Minipreparation Method Suitable for AFLP and Other PCR Applications - http://pubs.nrc-cnrc.gc.ca/ispmb/ispmb17/17053-1.pdf
Preparation of DNA from plant tissues suitable for PCR methods including AFLP, article by DH CHEN and PC RONALD Department of Plant Pathology, University of California, Davis.
Adjuvants in PCR Reactions - http://info.med.yale.edu/genetics/ward/tavi/p16.html
Brief discussion of additives to improve amplification efficiency and specificity of PCR, by Octavian Henegariu, Yale-New Haven Medical Center.
Amberg Laboratory Protocols: - http://www.upstate.edu/biochem/amberg/protocols.php
Laboratory protocols for PCR work used by the group of David Amberg at the Department of Biochemistry and Molecular Biology Upstate Medical University, Syracuse, New York.
Anchor Probes for Comparative Mapping of Grass Species - http://greengenes.cit.cornell.edu/anchors/
Article in which probes from different libraries were used to hybridize seven cereals at the Department of Plant Breeding and Biometry, Cornell University, NY.
Attotron Biosensor Corporation - http://www.attotron.com
Research and development company for development of biosensors and related products for the research and educational markets.
BioRad, Amplification, PCR - http://www.bio-rad.com/B2B/BioRad/product/br_category.jsp?
Division of BioRad Laboratories that manufactures and sells instruments for PCR, in Hercules, California, USA.
Degenerate PCR - http://www.dartmouth.edu/~ambros/protocols/other/koelle/degenerate_PCR.html
The identification of novel members of gene families by PCR using degenerate primers is described and protocols given. Article by Michael Koelle 1996 on the web site of Dartmouth College.
Detection of Point Mutations by RFLP of PCR Amplified DNA Sequences - http://www.uni-graz.at/~binder/thesis/node64.html
Thesis abstract about restriction fragment length polymorphism (RFLP) by Alexander Binder 1997.
Detection of Single Nucleotide Mutations in Wheat Using Single Strand Conformation Polymorphism Gels - http://pubs.nrc-cnrc.gc.ca/ispmb/ispmb19/R01-013.pdf
P Martins-Lopez, H Zhang, R Koebner, Plant Mol. Biol. Reporter 19(2001): 159-162. From National Research Coouncil Canada.
DNALC: PCR Animation - http://www.dnalc.org/ddnalc/resources/shockwave/pcranwhole.html
An animation explaining how the Polymerase Chain Reaction (PCR) works, from the Dolan DNA learning center, Cold Spring Harbor Laboratory, USA.
Dolan DNA Learning Centers Gene Almanac - http://www.dnalc.org/home.html
Educational site on topics in genetics and gene expression from Cold Spring Harbor Laboratory, USA.
Effect of PCR Buffer on Multiplex PCR - http://www.qiagen.com/literature/brochures/pcr/pdf/pcrcha03.pdf
Multiplex PCR employs different primer pairs in the same amplification reaction. This requires extensive optimization of annealing conditions. From Quiagen (company).
Fidelity of DNA Polymerases for PCR - http://www.lecb.ncifcrf.gov/~pnh/papers/TIBS/aug95.html
Article by PN Hengen from TIBS 1995
FISH Guide and Troubleshooting - http://info.med.yale.edu/genetics/ward/tavi/FISHguide.html
Links to pages describing influential parameters, with guides on PCR, RT-PCR and multiplex PCR reactions, Taq, FISH, CM-FISH, TM-FISH, microarrays, CCK, slide prep and labeling, maintained by Octavian Henegariu from Yale University, New Haven, CT.
Fluorescence in Situ Hybridisation - http://info.med.yale.edu/genetics/ward/tavi/FISH.html
Technical notes on Fluorescence in situ hybridisation from the Institute of Genetics of Yale School of Medicine, New Haven, Connecticut, USA.
GeneOhm Sciences - http://www.geneohm.com
Tests on group B Streptococcus and methicillin resistant Staphylococcus aureus by PCR / DNA sequencing.
GenHunter - http://www.genhunter.com
Manufacturer of material for differential display PCR in Nashville, Tenn USA.
HiFi DNA - http://www.hifidna.com/
HiFi DNA is a company selling a DNA polymerase for PCR at low temperature giving accurate replication of certain sequences where Taq fails.
Ingenetix GmbH - http://www.ingenetix.com/
Develops technology and products for DNA and mRNA research. Also provide DNA testing for the determination of parentage/paternity and custom DNA sequencing, oligonucleotide synthesis, genotyping services, pharmacogenetics and quantitative PCR, in Vienna, Austria.
Inverse PCR and Cycle Sequencing of P Element Insertions for STS Generation - http://www.fruitfly.org/about/methods/inverse.pcr.html
Step by step protocol, by EJ Rehm, Berkeley Drosophila Genome Project, USA.
Inverse PCR for PAC-end Sequencing - http://www.genetics.wustl.edu/fish_lab/frank/cgi-bin/fish/prot2.html
To generate PCR fragments that contain the ends of PAC inserts that can be sequenced. Protocol by B Barbazuk, Washington University Zebrafish Genome Resources Project, USA.
Inverse PCR for Use with Snyder mTn-lacZ/LEU2-based Mutagenesis - http://labs.fhcrc.org/gottschling/General%20Protocols/ipcr.html
Protocol by M McMurray, Fred Hutchinson Cancer Research Center, Seattle, Wa. USA.
Inverse PCR Protocol - http://www.mcdb.lsa.umich.edu/labs/maddock/protocols/PCR/inverse_pcr_protocol.html
Step by step protocol, from the web site of the Department of Biology, University of Michigan, USA.
Kary B. Mullis - Autobiography - http://nobelprize.org/chemistry/laureates/1993/mullis-autobio.html
The originator of PCR, from the Nobel e-museum web site.
Kary Mullis - http://www.invent.org/hall_of_fame/109.html
Inventor Profile of Kary Mullis, the originator of PCR, from the National Inventors Hall of Fame web site.
Long PCR Protocol - http://twod.med.harvard.edu/labgc/estep/longPCR_protocol.html
Protocol and guidelines for choice of conditions for PCR of long sequences (10 kb or larger). From Genetics Dept., Harvard Medical School, Boston, MA, USA
Nematode ITS1 Size Variation - http://nematode.unl.edu/its_id/EXAMPLES/index.htm
Examples of Restriction Fragment Length Polymorphism (RFLP)electrophoresis slabs for different nematodes, from University of Nebrasca.
Optimizing Multiplex and LA-PCR with Betaine - http://www-lecb.ncifcrf.gov/~pnh/papers/TIBS/jun97.html
LA-PCR = "long and accurate PCR". Article by PN Hengen in TIBS June 1997.
Optimizing PCR Protocols - http://www.jax.org/imr/optimize_pcr.html
Brief guidelines. From the Jackson Laboratory, University of Maine, USA.
PCR Amplification of cDNA Segments by 2 Stage Nested PCR - http://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?type=method&method_id=555
Protocol from the method database of NIH, USA.
PCR and Multiplex PCR Guide - http://www.info.med.yale.edu/genetics/ward/tavi/Guide.html
Discussions of the parameters influencing the PCR reaction and some PCR and multiplex PCR applications, by Octavian Henegariu on the web site of the Yale - New Haven Medical center.
PCR Animated - http://users.ugent.be/~avierstr/principles/pcrani.html
Animation illustrating the principle of PCR, from the University of Ghent, Belgium.
PCR Gateway - http://www.horizonpress.com/pcr/
A directory of PCR techniques, PCR protocols, PCR troubleshooting, PCR websites and online resources from the publisher Horizon Press.
PCR Guru - http://www.pcrguru.com/
A downloadable textbook on PCR setup and optimization, not free.
PCR Method Protocols - http://hg.wustl.edu/hdk_lab_manual/pcr/pcrcontents.html
Protocols for PCR posted by the Helen Donis-Keller Laboratory.
PCR Primer Design and Reaction Optimisation - http://web.uct.ac.za/microbiology/pcroptim.htm
Article by Ed Rybicki, Department of Molecular and Cell Biology, University of Cape Town in: Molecular Biology Techniques Manual, on the web site of the University of Cape Town.
PCR Project - http://sunsite.berkeley.edu/biotech/pcr/
Presentations from the University of California at Berkley on PCR, both current research reports and reviews.
PCR Protocol - http://www.mcdb.lsa.umich.edu/labs/maddock/protocols/PCR/general_pcr_protocol.html
Detailed PCR protocol from the web site of the Department of Biology, University of Michigan, USA.
PCR Protocols - http://www.cas.psu.edu/docs/CASDEPT/VET/jackvh/jvhpcr.html
Protocols and technical hints, particularly for reverse transcription PCR, somewhat outdated, compiled by Dr Jack Vanden Heuvel, Department of Veterinary Science and Molecular Toxicology Program, Penn State University
PCR Technology - http://www.accessexcellence.org/LC/SS/PS/PCR/PCR_technology.html
An introduction by Connie Veilleux from the US National Health Museum website.
PCR Troubleshooting - http://info.med.yale.edu/genetics/ward/tavi/Trblesht.html
Limited to conventional straight forward PCR. Page designed and maintained by Octavian Henegariu on the web site of the Yale - New Haven Medical Center.
PCR World - http://pcrworld.blogspot.com
Collection of unreferenced texts on various aspects of PCR.
PCR-ELISA and Related - http://www.btc-bti.com/pcrelisa.htm
P Zhang, CJ Gebhart, D Burden, GE Duhamel: A low technology alternative to real time PCR, technical article on the site of BT&C, Inc Bridgewater, NJ, USA.
Polymerase Chain Reaction - http://www.accessexcellence.com/RC/CT/polymerase_chain_reaction.html
Popular survey article by Mark V. Bloom, DNA Learning Center, Cold Spring Harbor Laboratory, from the web site of the US National Health Museum.
Polymerase Chain Reaction (PCR) - http://www.accessexcellence.org/AB/GG/polymerase.html
A graphic description of the principle of PCR from the US National Health Museum web site.
PrimerDigital - http://primerdigital.com/index.php
International biotechnology company specialized in a design service for PCR primers and probes, PCR-based technology development, projects for development of polymorphism and software development.
Primerfox - http://www.primerfox.com
Free online tool for generation of PCR primers.
Principle of PCR - http://users.ugent.be/~avierstr/principles/pcr.html
Applications in work on aging of Caenorhabditis elegans and phylogeny of nematodes, by Andy Vierstraete, Department of Biology, University of Ghent, Belgium.
Protocols Online: PCR Protocols - http://www.protocol-online.org/prot/Molecular_Biology/PCR/
Extensive collection of PCR protocols and methods from Protocol On Line.
Quantitative PCR Protocol - http://www.jax.org/cyto/quanpcr.html
From the Jackson Laboratory, University of Maine, USA.
RAPD PCR - http://avery.rutgers.edu/WSSP/StudentScholars/project/archives/onions/rapd.html
RAPD stands for Random Amplification of Polymorphic DNA, where the target sequence(s) (to be amplified) is unknown.Brief description, from Rutgers University, USA.
Rational Primer Design Greatly Improves Differential Display-PCR (DD-PCR) - http://nar.oxfordjournals.org/cgi/content/full/25/11/2239
Article: D Graf, AG Fisher, M Merkenschlager: Nucl. Acids Res. 25:11 2239-2240.
Reference in PCR - http://www.gene-quantification.org
Technical aspects of quantitative real-time PCR and RT-PCR. Instruments, kits, dyes, chemistries, and services presented by their manufacturers.
Rep-PCR Genomic Fingerprinting - http://www.msu.edu/user/debruijn/
Bacteria are characterized by Rep-PCR fingerprinting using primers corresponding to naturally occurring repetitive sequences in the interspersed regions.
RFLP Definition - http://vm.cfsan.fda.gov/~frf/rflp.html
RFLP = Restriction Fragment Length Polymorphism, from FDA
Roe Laboratory Protocols - http://www.genome.ou.edu/proto.html
Molecular biological protocols, mostly PCR related used by Bruce A. Roe at the Dept. of Chemistry and Biochemistry, OU, Norman, OK.
Single Tube Confirmation PCR Protocol - http://www-sequence.stanford.edu/group/yeast_deletion_project/single_tube_protocol.html
For characterization colonies of transformed clones of Saccharaomyces, from the web site of the Stanford Genome Technology Center, Palo Alto, CA, USA.
Standard PCR Protocols - http://web.uct.ac.za/microbiology/pcrcond.htm
From Molecular Biology Techniques Manual, from the web site of the University of Cape Town, South Africa.
T-DNA Generated Enhancer Traps in Arabidopsis - http://www.dartmouth.edu/~tjack/
Application of inverse PCR, partial genomic libraries and TAIL-PCR in cloning flanking, at the Department of Biological Sciences, Dartmouth College, Hanover, NH.
Tavi's PCR Protocols - http://info.med.yale.edu/genetics/ward/tavi/PCR.html
A page describing the main parameters and trouble-shooting in PCR. The page is somewhat dated (updated 1997) but still useful.
The PCR Encyclopedia - http://www.pcr-encyclopedia.com/
Describes plans for a free encyclopedia dedicated to the polymerase chain reaction (PCR).
The Web Guide of PCR - http://www.pcrlinks.com/
List of links and forum on the subject and related methodology. Set up and maintained by SJ Krivokapich, National University of Misiones, Argentina.
Thermostable DNA Polymerases - http://arbl.cvmbs.colostate.edu/hbooks/genetics/biotech/enzymes/hotpolys.html
Discussion of their origin and briefly their properties. From the web site of Colorado State University.
Wayward PCR Primers - http://www-lecb.ncifcrf.gov/~pnh/papers/TIBS/jan95.html
Article by PN Hengen from TIBS 1995 on the loss of activity of PCR primers with time.
What the Heck is PCR? - http://people.ku.edu/~jbrown/pcr.html
Popular description of the PCR technique by John C Brown, University of Kansas 1995.
Which DNA Marker for Which Purpose? - http://webdoc.sub.gwdg.de/ebook/y/1999/whichmarker
Compendia of the Research Project "Development, optimisation and validation of molecular tools for assessment of biodiversity in forest trees", European Union DGXII Biotechnology FW IV Research Programme. From the web site of the University Library, Göttingen.
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