Genome Project Workshop
Smith College

30/3/97-4/4/97

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The report of the meeting is available here

1 The EST Effort

Crosscreening cDNA Libraries and in depth analysis of sequences

This section will have two components: making gridded libraries and crosscreening them, and "bioinformatics" - looking at the sequences and understanding their "meaning".

2 The Genome Map

Building a genome map by hybridisation

This section will look at the construction of genome libraries, screening of the gridded libraries and generation of a physical map from the hybridisation data.

INFORMATICS

Sessions on

• analysis of cDNA sequence using the world wide web and email
• searching databases and understanding the output
• following up leads and looking in-depth at particular sequences
• "clustering" EST sequences by sequence identity
• the genome database FilDB
  • there are two basic introductions (one from Jean Thierry-Meig/Richard Durbin, the program's authors and one from Sam Cartinhour)
  • The best introduction is the ANGIS Handbook
• the bibliographic resource BiblioFil

GRIDDING LIBRARIES and MAKING FILTERS

We will pick colonies to microtitre plates and make gridded filters for crosscreening.

Mass Excision of lambda Zap II Libraries: General Protocol from Stratagene

Titration of Mass Excised Phage

The "Hedgehog" 96 well picker and making a jig to print 384 colonies to a plate

Picking to Grid Plates and Replicating Grids

Method for Making Grids

Regridding

An Introduction to Genome Mapping

NONRADIOACTIVE SCREENING OF FILTERS

We will use two nonradioactive methods (NEB and Amersham) for crosscreening the filters. We will both simgle-clone probes, pooled probes and end-probes.

Making Probes from EST Clones

Amersham Nonradioactive Probing Method

NEB Phototope Method

NEB CDP-Star Detection Method

Making End Probes from Clones

Just for the record here's the Radioactive Screening Method