Molecular Biology Protocols 30 slide in situ ABI 96-well load ABI sequencing (old) BAC Fingerprinting BACs For Microinjection BAC Modification BAC prep + sequencing BAC Screen Bacteria to in situ probe Cell Death and Proliferation CHEF Gels Cleaning DNA for transcription Competent Cells Large Scale CsCl plasmid prep Microsatellite Library Paraffin in situ SIte Directed Mutagenesis Sequencing PCR products Southerns-Classic TENS miniprep (bacteria) Transcription Transforming Bacteria

Kingsley Lab Protocols & Web Links

Mouse Protocols Blue/Red Skel preps (adult) Fixation and Decalcification Fixation and Sucrose embedding Genotyping by PCR Histology Immunohistology LacZ Stain - embryos LacZ - nuclear fast red staining PCR for Gdf6 and Gdf7 PCR for GDF5 and LacS PCR for short-ear (se) Standard Sectioning for Staining Whole Mount Immunohistochemestry Whole Mount in situ

Fish Protocols (Stickleback) BAC Screen DNA prep Fixation In Situs In Vitro Transcription Microsatellite Genotyping Microsatellite Library Skeletal Preps Stickleback Care Stickleback Collection Stickleback Parasites

Web Links

Bio-Informatics Tools (Sequence analysis)

• BCM Search Launcher
• Block-Maker (Design Blocks and a Cobbler sequence from known sequences)
• Decypher (TimeLogic Server) (Use this if the Stanford Server is down)
• DoubleTwist
• eMotif and eBlocks
• End sequence info for mouse BAC clones (TIGR...input ID# of BAC)
• ExPasy - Protein Analysis Tools (THIS PAGE HAS A TON OF RESOURCES !!!)
• GENSCAN (MIT)
• InterPro (Get a FULL profile for your protein - Checks BLOCKS, PRINTS, PRODOMO, DOMO, and PFAM databases)
• MarFinder (Find putative matrix attachment sites in genomic sequences)
• Pipmaker
• ProSite
• PSORT
• Repeatmasker (Institute for Systems Biology)
• Swiss-Prot
• Stanford's SeqWeb (GCG package available thru Stanford's PMGM web interface)
• Transport Protein Database and Tools
• Whitehead Institute (MIT) (Genomic Markers etc.)

Journal Resources

• Cell
• Development
• Developmental Dynamics
• Genes & Development
• Highwire Press
• Nature
• Science
• Socrates (Stanford Online Catalog)
• Stanford's online BIOLOGY JOURNALS
• SciSearch (Has a citation index - complete bibliographies of each reference and lists of papers that cited the reference)

Model Organisms

Mouse

• UCSC Mouse Genome Browser
• Embryo Images on-line
• The Edinburgh Mouse Atlas Project
• µMRI Atlas of Mouse Development
• Mouse Genome Informatics
• Jackson Labs
• Mouse Genetics - Lee Silver
• The Trans-NIH mouse initiative (Has links to various stuff, including the mouse BAC sequencing program)
• The Whole Mouse catalog (A nice site with links to lots of mouse information/resources/protocols)
• The Visible Mouse (UC Davis with NMR images, histology series in quicktime format)

Stickleback

• UCSC Stickleback Genome Browser
• Broad Institute Stickleback Genome Information
• Dolph Schluter

Other

• UCSC Pufferfish Genome Browser
• Pufferfish genome

Protocols

• Protocols-online

Skeletal Biology and Anatomy

• The "ONLINE SKELETON"
• Human Osteology site (Cool 3D computer-generated reference images of the human skeleton)

Stanford Sites

• CMGM software resources
• SUPD (stanford's postdoc organization)