Parallel Biological Systems

This research program is centered at the Massachusetts General Hospital, Harvard Medical School, with bioinformatics participation from the Boston University Biomedical Engineering Department and the Genetics Department at Harvard Medical School. The investigators in the program are working to identify and characterize gene networks activated by pro-inflammatory, metabolic, and pathogen stresses that affect the cardiovascular system and the lungs.

	MGH-PGA BASE Plug-in Suite	A number of plug-ins written for the BioArray Software Environment provide it with a greatly expanded ability to analyze microarray expression data.
	MGH-PGA Proteomic Tools	Our database is based on NCBI's protein database, with additional information about the DNA coding sequences. It allows identification of the DNA coding sequences by searching for peptide sequences. You may also upload a protein file and get the corresponding DNA coding sequences, as well as primers designed for PCR.
	OligoPicker	OligoPicker selects up to five oligo probes for each of the DNA sequences you provide for microarray printing. OligoPicker picks specific oligos by skipping regions with contiguous bases common in other sequences. In addition, oligo specificity is double-checked by BLAST.
	Oligo List Builder for Synthetic Genes	Need descriptive text...
	PrimerBank	PrimerBank is a public resource for PCR primers. These primers are designed for gene-expression detection or quantification (real-time PCR). PrimerBank contains about 180,000 primers covering most known human and mouse genes.
	Web Edit	This program can facilitate the assembly of new plasmid sequences by turning map sequences into raw DNA fragments.
	Web Map	This program creates flexibly formatted sequence maps from a variety of inputs, including GenBank pages formatted as either text or html. The maps are hyperlinked to GenBank resources and present expository information through popup windows. A very large number of style options are available to display SNPs, open reading frames, and restriction enzyme cleavage sites.

Materials

Over the years, the Seed laboratory has provided research materials upon requests as a professional courtesy. These materials include recombinant DNAs, cell lines, and mice. To request plasmids or materials, send your request with a complete mailing address via email or fax to Brian Seed. The request should contain the following assertion: The materials received are for research use only and will not be used for commercial purposes without the prior written consent of Massachusetts General Hospital. Please avoid phone requests; they have a tendency to get lost.

Below are selected sequences of highly-demanded DNA plasmids and their related protocols. The Webmap software listed above may assist you in mapping the plasmid sequences.

Recombinant DNA Plasmids
Names of vectors using SupF system for selection: pCDM and pPACEBV
Names of vectors using Amp resistance for selection: pCDNA3, pRX, pPEAK

Protocols
Panning (method for expression cloning)
High-efficiency transformation in E. coli
DEAE dextran transfection
Propagation of suppressor tRNA plasmids

IgFusionProteins
Peak13CD5Lnegl

RIP
RX
humanRIP
murineRIP

HIV
Peak10-Syngp160mn