Human Protein Atlas

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Module 2: PrEST-design

Principal Investigator (PI): Lisa Berglund

Personnel: Dr Åsa Sivertsson, Linn Fagerberg (PhD-student) and Johan Rockberg (PhD-student)

Responsibility: To initiate the Human Protein Atlas (HPA) analysis of human proteins by in silico selection of Protein Epitope Signature Tags (PrESTs). For each PrEST an oligonucleotide primer pair suitable for subsequent cloning procedures is designed and ordered.

Description: The PrEST design module performs computer-based analysis of protein sequences for selection of protein fragments (PrESTs). The PrESTs should be suitable as immunogens for generation of specific polyclonal antibodies to target gene products.

For each selected protein fragment, a PrEST-specific oligonucleotide primer pair is designed to be used for cloning of the corresponding gene fragment by RT-PCR in the Molecular Biology module.

Information requested by the HPA laboratory concerning the PrEST and its corresponding gene is collected and stored in the HPA database. Each PrEST is followed through the HPA pipeline and results from different modules are continuously analyzed. The protein fragment selection strategy is further developed in order to improve downstream success rates.

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