Van Oudenaarden Lab:Internal

Image Processing Tools

Reagents list Restriction enzymes (-20C fridge) Chores list Books in the lab Single Molecule FISH

Checklist for 68-311 tissue culture room maintenance:

Mark empty CO2 tanks

Fill out log sheet for CO2 tanks

Emergency contact information:

Chris Ng, Fraenkel Lab 68-317

cwng@mit.edu

253-2042

Deepika Dinesh, Fraenkel Lab 68-317

dpk_d@mit.edu, db21gn@gmail.com

452-2086

Yanna Zheng, AvO Lab 68-353

617-955-6488

Other TC facilities in building 68:

Burge Lab

Lab phones: 253-7039, 253-6726

Online tools: NebCutter V2.0 Restriction and other DNA analysis, with great GUI.

Primer3 Primer design tool best for creating compatible primer pairs for a given template. Netprimer Primer test tool. Verify melting temperatures, hairpins, dimerization, &c of final primer designs.  NCBI National Center for Biotechnology Information  Entrez Biology search engine, e.g. for looking up protein and DNA sequences by name PubMed Literature search BLAST Basic Local Alignment Search Tool, for DNA/protein alignment and comparison, primer verification, etc. Google Scholar Most general literature search tool.

Freeware: WinGene Tool for analyzing nucleotide sequences. Best for reverse complements and primer checks. MFI For converting flow cytometer output files to ASCII. Simple free registration. OpenOffice.org Open source office environment, fully compatible (well, almost) with MS Office, including Powerpoint. Open Perl IDE Open source Integrated Development environment for Perl. Easy to set up and use. ActivePerl Easy installation for running Perl scripts in Windows; necessary for Open Perl IDE.

Perl scripts: deannotate_dna.pl A useful script for annotating and editing DNA sequences. This file provides documentation and an example. cytometry.zip Package of scripts and executables for quickly processing raw flow cytometer files into a table of histograms. Consult Michael on its use.

Protocols: General E. Coli Yeast Cyanobacteria

additions, corrections, &c: [mailto:mokelly@mit.edu ]