Genome Biology Unit (GBU) Institute of Biotechnology, Viikki Tea Vallenius, Kaisa Laajanen, Niina Roine Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies Content General view Description of our libraries Basics of Gateway cloning How to order Clones and cloning service Future plans (e.g. kinome sets, custom projects) Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies http://www.biocenter.helsinki.fi/bi/gbu/ Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies GBU services 2011 - 2013 28 research groups of which 12 represent new groups in 2013 Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies cDNA/ORF sets available through Genome Biology Unit MGC Collection. cDNA library Human 20 945 Mouse 8 290 ORFeome Collaboration. Full ORFs Human 16 934 Mouse 1 758 Value for scientists in Finland! reduced costs rapid delivery easy access screening possibilities Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

MGC collection = Mammalian Gene collection http://mgc.nci.nih.gov/ ORF 5’ UTR 3’ UTR National Institutes of Health initiative started 2001. The aim was to generate full-length protein coding cDNAs for human and mouse genes sequence validated MGC clones were intially obtained by random EST-screening of cDNA libraries - From the practical point of view: *clones we have are in various vectors -> not necessarily suitable for your studies immediately -> more time-consuming & expensive to transfer to other vectors *full length cDNA clones -> may contain 5’/3’ UTRs, which may have a regulatory role Sequenced from N terminus by the vendor Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

The ORFeome collection ORFeome Collaboration, which aim is to provide sequence validated, ORF clones in Gateway entry vectors allowing easy transfer of the ORF sequences into various expression vectors many available either with or without stop codons From the practical point of view: *prior to expression studies need to be transferred into destination vectors *easy to transfer to any destination vector using Gateway cloning *contain only the protein coding sequences *GBU’s library has been intially validated Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies Basics of the Gateway technology: Generation of an entry clone I. BP reaction = “ insert your gene of interest into the Gateway Technology” 2. negative selection ORF 1.site-specific recombination kana 3. specific enzyme Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies Basics of the Gateway technology: Generation of an entry clone I. BP reaction = “ insert your gene of interest into the Gateway Technology” 2. negative selection ORF 1.site-specific recombination kana 3. specific enzyme entry clone ORF Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Cloning service provided by GBU! Basics of the Gateway technology: Generation of an expression clone 2. LR reaction = “ transfer your gene of interest into destination vectors” 2. negative selection ORF 1.site-specific recombination amp 4. antibiotic selection 3. specific enzyme = OFR library Cloning service provided by GBU! Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies Basics of the Gateway technology: Generation of an expression clone 2. LR reaction = “ transfer your gene of interest into destination vectors” 2. negative selection ORF 1.site-specific recombination amp 4. antibiotic selection 3. specific enzyme Several advantages: - rapid to perform - efficient : > 90% success rate - universal : no need to consider cloning sites reversible : entry -> destination -> entry Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies Content General view Description of our libraries Basics of Gateway cloning How to order Clones and cloning service Future plans (e.g. kinome sets, custom projects) Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies http://www.biocenter.helsinki.fi/bi/gbu/ Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

How to order: available ORF/cDNA sets Available clones on excel sheets Ordering form Sequence your clones easily Collaboration with DNA sequencing and Genomics laboratory in Viikki and Biomedicum Sequencing Unit (BSU) Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

How to order: available ORF/cDNA sets Available clones on excel sheets Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

How to order: ordering form Available clones on excel sheets Ordering form Sequence your clones easily Collaboration with DNA sequencing and Genomics laboratory in Viikki and Biomedicum Sequencing Unit (BSU) Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

How to order: we recommend to verify you clones Available clones on excel sheets Ordering form Sequence your clones easily Collaboration with DNA sequencing and Genomics laboratory in Viikki and Biomedicum Sequencing Unit (BSU) Primers available for verification of ORF clones Petri Auvinen Lars Paulin Order clones through ordering form. Find your clone of interest through the excel (pay attention to vector, stop codon status) Tapio Tainola Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies ORF cloning service We clone your ORF clones of interest to multiple Gateway destination vectors Cloning format: Single clones or 96-well format Remember: FuGU can provide viral particle production service from your lenti-viral constructs Mammalian Expression Bacterial Expression Insect Expression Entry Clone Most commonly used Gateway destination vectors: N- terminal GST N- terminal 6xHis C- terminal V5 + 6xHis C- terminal GFP Lenti vector with C- term V5 Stop N-terminal emGFP + C- term V5, C-term emGFP N- and C- term. mCherry (a kind gift from Maria Vartiainen) Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

96-well cloning and transfections trials Custom projects To be separately agreed Cloning to the customers destination vector, dest-entry-dest Primer script to design primers with Gateway tails We are not making vector modifications. Everything else we want to think Kinome: Collection of functional Kinome sets under process/ongoing Creating the sets corresponding the kinome by FIMM Overlap FIMMin kanssa N-emGFP Pictures taken with Cell Insight in Light Microscopy Unit (LMU) Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies Future Plans GBU/FIMM/FuGU joined forces: GBU is currently generating human Kinome ORFs (FIMM & FuGU have kinome knockdown reagents) Custom projects Custom-tailored Gateway clonings Primer script to design primers with Gateway tails If you have ideas, we are happy to discuss Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies New service available - 3DHISTECH Pannoramic digital slide scanner Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies New service available Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014

Genome scale reagents and services for functional studies Genome Biology Unit Contact information: Phone: 09-19159429 Email: bch-gbu@helsinki.fi Web pages: www.biocenter.helsinki.fi/bi/gbu Personnel: Niina Roine M Sc Kaisa Laajanen M Sc Tea Vallenius MD, PhD Genome Biology Unit Institute of Biotechnology Genome scale reagents and services for functional studies 22.01.2014