Genotyping & Phenotyping Technology Projects & Protocols

Latest Update: 1-Jun-1999 by GMC , reyes@rascal.med.harvard.edu , Up to: Church Lab page

Phenotyping and Genome Engineering

• Dereth Phillips, Joyce Liu, Jay Shah, and Andy Link, Pam Ralston
• pKO3 vector and Homologous Recombination General Mutation Substitution Strategy
• Long-PCR Protocol
• E.coli knockout project status (** updated 19-Oct-1998**)
• Multiplex knockout strain pool competition readout methods

E.coli & Yeast Genome-wide RNA Expression Analyses

• Pete Estep, Fritz Roth, Jason Hughes, Doug Selinger, Barak Cohen, Martha Bulyk, Martin Steffen
• Commercial sources
• Yeast Expression Data and Motif Software (27-Oct-1998)

New Solid Phase Synthesis strategies:

• Mosaic Technologies Corp. (Boston, MA)

Primer Station 960- 96 Channel Parallel DNA Synthesizer

• Intelligent Bio-Instruments Inc. (Cambridge, MA)
• HMS/HHMI Biopolymers Facilities

Single Pore Conductance DNA Analysis

• Kasianowicz et al.  (1996) Proc Natl Acad Sci USA 93:13770-3. Characterization of individual polynucleotide molecules using a membrane channel.
• Church, G.M., Deamer, D.W., Branton, D., Baldarelli, R., Kasianowicz, J. (1998) US Patent # 5795782: Characterization of individual polymer molecules based on monomer-interface interactions.

Multiplex DNA Analyses and Molecular Tags

• Multiplex Sequencing 1988 Church and Kieffer-Higgins
• Multiplexed biochemical assays with biological chips.1993 Fodor et al.
• Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. 1996 Shoemaker et al.
• University of Utah 1994 Mapping automation
• Genome Therapeutics Corp.: Methanobacterium thermoautotropicum genome sequence
• Max-Delbrück-Centrum für Molekulare Medizin: Human polymorphisms
• NIST-ATP: Diagnostic Laser Desorption Mass Spectrometry Detection of Multiplex Electrophore Tagged DNA
• Bruker Analytical Systems Inc. (Billerica, MA)
• Northeastern University
• Harvard Medical School
• Genome Therapeutics Corp.
• Harvard Medical School Machine Shop

Our funding sources over the years and related sites:

• LSRF Life Sciences Research Foundation (& Monsanto)
• NIST-ATP National Institutes of Standards and Technology Advanced Technology Program
• NIH-NHGRI National Human Genome Research Institute
• ONR Office of Naval Research
• NSF National Science Foundation
• NLM National Library of Medicine
• HHMI Howard Hughes Medical Institute - Genetics Program
• DOE Department of Energy - Genome Information
• DARPA Defense Advanced Research Projects Agency
• Hoechst Marion Roussel
• Rhone-Poulenc Rorer
• Lipper Foundation 

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• Genome Centres
• ABRF Association of Biomolecular Resource Facilities