The Centre for Applied Genomics

Genome Resource Facility Library Index

Genomic Libraries

RPCI-11 Human BAC Library (Canadian research community only)

The RPCI-11 human BAC library was constructed in the laboratory of Pieter deJong at the Roswell Park Cancer Institute in Buffalo, NY. http://bacpac.chori.org/

TCAG has all four segments of the library (plates 1-1152).

For library screening provide a minimum of 500ng of gel-purified vector and repeat-free probe.

RPCI-1 Human PAC Library (Canadian research community only)

The RPC-1 human PAC library was constructed in the laboratory of Pieter de Jong at the Roswell Park Cancer Institute in Buffalo, NY. http://bacpac.chori.org/

TCAG only has filters and clones for segment one of the PAC library (plates 1-321).

For library screening provide a minimum of 500 ng of gel purified vector and repeat-free probe. Positive clones will be sent to the requesting investigator as an agar stab by regular mail, unless a Fedex account is provided.

RPCI-22 Mouse BAC Library (Canadian research community only)

The RPCI-22 129/SvEvTACBr BAC library was constructed in the laboratory of Pieter de Jong at the Roswell Park Cancer Institute in Buffalo, NY. http://bacpac.chori.org/. This is a library to screen for making mouse 129 knockouts.

TCAG only has filters for segment 2 of the mouse BAC library. The clones are ordered on an 'as needed' basis.

RPCI-23 Mouse BAC Library (Canadian research community only)

The RPCI-23 (C57BL/6J) Mouse BAC library was constructed in the laboratory of Pieter de Jong at the Roswell Park Cancer Institute in Buffalo, NY. http://bacpac.chori.org/. This is a library is in the process of having the ends of the BAC sequenced and is used for mapping purposes.

TCAG has both segments of the library (plates 1-480).

RPCI-81 Canine BAC Library (Canadian research community only)

The RPCI-81 Male (Doberman Pinscher) Canine BAC library was constructed in the laboratory of Pieter de Jong at the Roswell Park Cancer Institute in Buffalo, NY. http://bacpac.chori.org/.

TCAG only has the filter set for this library. The clones are ordered on an "as needed" basis.

RPCI-44 Porcine BAC Library (Canadian research community only)

The RPCI-44 Male Porcine BAC library was constucted in the laboratory of Pieter de Jong at the Children's Hospital Oakland Research Institute http://bacpac.chori.org/.

TCAG only has the filter set for this library. The clones are ordered on an "as needed" basis.

CEPH-Genethon Mega YAC Library

The CEPH-Genethon Mega YAC library was constructed at CEPH-Genethon in Paris, France. TCAG has the entire Mega YAC library.

Chromosome 7-Specific YAC Library

The Human Chromosome 7-specific YAC library was constructed from human/hamster hybrid DNA by Dr. Steve Scherer at the Hospital for Sick Children. It represents 5x coverage of chromosome 7.

Human Chromosome 7-specific cosmid Libraries

TCAG has two chromosome 7-specific cosmid libraries. One was constructed at the Lawrence Livermore National Laboratory (LLNL) and the other was constructed through the Imperial Cancer Research Fund (ICRF). Information on the libraries can be found at their respective websites; www.icnet.uk/public.html.

To have either library screened, provide a minimum of 500ng of gel purified vector and repeat-free probe. Positive clones will be sent to the requesting investigator as an agar stab by regular mail, unless a Fedex account is provided.

Mammalian Gene Collection

The Mammalian Gene Collection (MGC) contains 14,000 full-length human cDNA clones that have been sequenced-verified. Each sequence is in Genbank with unique MGC, I.M.A.G.E. and Genbank identifiers. For more information on these clones, see the Mammalian Gene Collection website at the National Institute of Health.

Hybrid Mapping

NIGMS Somatic Cell Hybrid Panel

The NIGMS somatic cell hybrid panel is a collection of human monochromosomal hybrids maintained in either hamster or mouse cell lines. We are currently using Panel #2. More information on the panel can be found at NIGMS.

To have the somatic cell hybrid screened a minimum of 5ug of each primer is required. For gene mapping, primers designed from the 3'UTR have the highest success rate for mapping with the hybrids. If possible, pretest the primers to ensure they amplify only human DNA and not rodent. If rodent DNA is amplified, the product size must be unique from that of human and be able to be resolved on an agarose gel.

Radiation Hybrid Panels

TCAG offers screening of three human radiation hybrid panels and one mouse radiation hybrid panel http://compgen.rutgers.edu/rhmap. A minimum of 30ug of each primer is required. For gene mapping, primers designed from the 3'UTR have the highest success rate for mapping with the hybrids. If possible, pretest the primers to ensure they amplify only human DNA and not rodent. If rodent DNA is amplified, the product size must be unique from that of human and be able to be resolved on an agarose gel.

Genebridge 4 Human/Hamster Radiation Hybrid Panel

The Genebridge 4 radiation hybrid panel consists of 93 hybrids of the whole genome. It was constructed in collaboration between the labs of Peter Goodfellow and Jean Weissenbach. It is estimated that 1 cR from this panel represents approximately 1000Kb. Further information on the G4 panel.

Stanford G3 human/Hamster Radiation Hybrid Panel

The Stanford TNG radiation hybrid panel consists of 83 hybrids for the whole genome. It was constructed at the Stanford Human Genome Centre. It is estimated that 1cR from this panel represents approximately 500Kb.

Stanford TNG Human/Hamster Radiation Hybrid Panel

The Stanford TNG radiation hybrid panel consists of 90 hybrids of the whole genome. It was constructed at the Stanford Human Genome Centre. It is estimated that 1cR from this panel represents approximately 10kb.

Mouse/Hamster Radiation Hybrid Panel

The mouse radiation hybrid panel consists of 100 hybrids and was constructed by Peter Goodfellow's lab at Cambridge University in the UK. DNA from the mouse strain 129aa was used.

FISH Mapping

FISH mapping of human phage, cosmids, BACs, PACs or YACs is offered for clone mapping and verification, deletion and duplication mapping and breakpoint analysis, inversion testing and high-resolution physical mapping. Please enquire for further details or with questions about doing a particular project.

NIA/NIH 15,000 Collection

Characteristics of NIA 15K Mouse cDNA Clone Set

~15,000 unique cDNA clones are derived from 52,374 ESTs from pre- and periimplantation embryos, E12.5 female gonad/mesonephros, and newborn ovary.
~80% of them are new.
~1.5 kb average insert size.
Clones were resequenced from their 3'termini to obtain longer reads and verify sequence. Sequence information is available at this Web Site. Clone names are from H3001A01 to H3159H12.
Click here to download 15k Fasta Formatted Sequences and List of Gene ID (Top Hits)
Handling of NIA 15k cDNA Clone Set
- includes Protocol for 2XYT Medium (with Glycerol)
- Preparation of DNAs for microarray.

NIA Mouse cDNA Database

For further information regarding this clone set, please check the NIA Mouse cDNA Project Home Page found at the following web site: http://lgsun.grc.nia.nih.gov/

TCAG has the complete NIA/NIH 15000 library collection.

For library screening provide a minimum of 500ng of gel-purified vector and repeat-free probe. Positive clones will be sent to the requesting investigator as an agar stab by regular mail, unless a Fedex account is provided.

Karyotyping

Karyotyping of human lymphoblasts (for research purposes only), rodent splenocytes and mouse embryonic stem cells is offered as a service in the TCAG cytogenetics facility. Please enquire for other species or cell types. Along with the karyotype, a complete summary of results is provided that lists the number of cells counted and karyotyped, the chromosome modal number and the number of atypical non-clonal cells (see sample report). For further information, please contact the facility.