Microarrays currently available from the BPFG:
BPFG Pan-Neisseria microarray-v2; Operon H. influenzae strain Rd / KW20 microarray; Kuipers / BPFG B. subtilis microarray; Operon N. meningitidis strain MC58 microarray; BPFG targeted group B streptococcus microarray; N meningitidis strain MC58 promoter microarray. Additional bacterial projects.
Eukaryotic system microarrays:
The BPFG / Dunn School mouse immunorray-v2; The BPFG / NDCLS microRNA-v2 microarray; Operon Mus musculus (mouse) AROS V4.0. Operon Rattus norvegicus (rat) V3.0. Operon Homo sapiens (human) V4.0.
Forthcoming microarrays (not yet tested or available, likely to be available in 2007):
Operon complete mouse microarray; Operon complete human microarray; Invitrogen complete mouse microarray; Invitrogen complete human microarray. For further information on these arrays, please contact Dr Nigel Saunders.
Externally sourced microarrays used with the BPFG:
MRC HGMP microarrays; Operon Arabidopsis microarrays; Operon Maize microarrays; Operon Rattus norvegicus (rat) V3.0; Operon Homo sapiens (human) V4.0.
Note: If you are considering a microarray for a particular experimental application, it is important to consider whether it is an adequate or optimal tool for your intended experiment. Any potential collaborations will include a discussion of this subject, and if necessary the formatting and replication of arrays may be modified where possible to generate a version of each chip more suitable for a given experimental question. For general information on this subject, potential array users are referred to the relevant sections of: Meaningful Microarrays.
The general (very unrestrictive) terms for supply of microarrays from the BPFG.
The Pan-Neisseria microarray-v2
This is an expanded version of the original pan-Neisseria array designed by the BPFG, produced by Prof. John Davies in Monash, with additional support form the 'Neisseria microarray consortium', including Profs: William (Bill) Shafer (Emory); H. Stephen Seifert (Chicago); David Dyer (Oklahoma); and Mike Apicella (Iowa). This original version of this microarray contains probes for N. gonorrhoeae strain FA1090, the strain MS11 gonococcal genetic islands, and N. meningitidis strains MC58 and Z2491, and is available from Prof John Davies, on a cost-recovery collaborative basis, on request. The version 2 pan-array contains a few (minimal) probe revisions, and additional probes for N. meningitidis strain FAM18, a range of strain-specific neisserial genes from GenBank, and some experimental / resistance marker probes. As well as being suitable for expression studies using the index / sequences strains, this array has been specifically designed to be suitable for comparative studies, both for comparative genome hybridization and expression studies. This microarray is available on a collaborative cost-recovery basis from Dr Nigel Saunders.
Further information on this array for existing and potential users, and those interpreting published data generated using it, and details of projects and publications that have used it.
The Operon H. influenzae strain Rd / KW20 microarray
This is a microarray fabricated with the commercially available C6-amine linked 70mer oligo probe set from Operon. This microarray is available on a collaborative cost-recovery basis from Dr Nigel Saunders.
Further information on this array for existing and potential users.
The Kuipers / BPFG B. subtilis strain 168 microarray
This is a microarray designed and fabricated in collaboration with the Kuipers group, at the Molecular Genetics group , at the Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands, and also for and with support from Prof. Jeff Errington, formerly of the Dunn School, and now director of the Institute for Cell and Molecular Biosciences, University of Newcastle. This is a non-linkered 70 mer oligo probe array designed for studies of the sequenced strain of B. subtilis . This microarray is printed in both Oxford and the Rijksuniversiteit Groningen. This microarray has been used and fully tested within the two groups that generated it, and while it is not currently published, it is available on a collaborative cost-recovery basis from Dr Nigel Saunders, and also from Professor Oscar Kuipers. This microarray should be considered specific to the strain to which it was designed, it is particularly suitable for expression studies in this and derived strains.
Further information on this array for existing and potential users.
The Operon N. meningitidis strain MC58 microarray
This is a microarray fabricated with the commercially available C6-amine linked 70mer oligo probe set from Operon. This microarray is available on a collaborative cost-recovery basis from Dr Nigel Saunders. This microarray should be considered specific to the strain to which it was designed, it is particularly suitable for expression studies in this and derived strains.
The Group B streptococcus targeted microarray
This microarray was developed to support, as a collaboration with Dr Mark Anthony (formerly Mark Herbert), who was a member of the Paediatrics Department, University of Oxford, and is currently a member of the Paediatrics Department, University of Birmingham. This microarray contains probes primarily for the known / annotated regulator proteins, surface proteins / virulence determinants, and those that differed between the first and second sequenced group B streptococcal genome sequences. This microarray is available on a collaborative cost-recovery basis from Dr Nigel Saunders.
Further information on this array for existing and potential users, and those interpreting published data generated using it, and details of projects and publications that have used it.
Additional bacterial projects:
We also have ongoing collaborative microbial microarray projects addressing genes in environmental pseudomonads (in collaboration with Dr Sarah Turner and Adrian Tett, CEH, Oxford) and Wolbachia (in collaboration with Dr Steven Sinkins and Dr Lisa Klasson, The Department of Zoology, Oxford). These arrays are not at a stage at which they are suitable for general use / availability. We are also in the planning stage for a focussed microarray for Rhodobacter spheroides, with Prof. Judy Armitage, Department of Biochemistry, Oxford.
We are open to the development of new project-directed microarrays, particularly if they can be made available to the research community, and are happy to discuss new projects of this type.
Additional, currently externally sourced microarrays, with which we have worked with and are interested in working with in future collaborations: The Operon E. coli strain K12 microarray. We have worked with this microarray from two sources, and currently for projects using these arrays, we source these from Dr Anthony Cornish, University of Alberta. For those wishing to perform studies on this species, we are happy to recommend this as a source, and are also able and interested in working on collaborative E. coli studies using these arrays.
Eukaryotic system microarrays.
The BPFG / Dunn School mouse immunorray-v2
This is a 70-mer oligo-based microarray addressing contains 1536 probes addressing around 1450 genes (there is some redundancy due to annotation revisions during the life of the array) focussed upon genes involved in immune responses and immune system cell development and differentiation. The first version of this array was fabricated in early 2005 and contained probes for 768 genes (this version of the array is no longer available). The second version of the array was completed in October 2006, and is available on a collaborative cost-recovery basis from Dr Nigel Saunders.
Further information on this array for existing and potential users, and those interpreting published data generated using it, and details of projects and publications that have used it.
The BPFG / NDCLS microRNA-v2 microarray
This is a positive stranded probe microRNA microarray produced in collaboration with Dr Charles Lawrie of the Nuffield Department of Clinical Laboratory Sciences, University of Oxford. This microarray includes probes for all known and predicted microRNAs from human, mouse, rat, and chicken, plus some additional viral and other probes. The first version of this microarray was fabricated in September 2005, to the then current microRNA databases at the Sanger Institute (this version of the array is no longer available). The second version of the microarray includes all of the original probes, plus all additional probes as contained in the databases up to miRBase v 9.0, October 2006. This version of this microarray is available on a collaborative cost-recovery basis from Dr Nigel Saunders.
Further information on this array for existing and potential users, and those interpreting published data generated using it, and details of projects and publications that have used it. More information on microRNAs and these microarrays from Dr Lawrie's 'microRNAworld' web page.
The Operon complete mouse (Mus musculus) AROS V4.0
This is a 70-mer oligo-based microarray addressing a relatively recent annotation of the mouse genome. Version 4.0 of the Mus musculus (mouse) AROS contains 35,852 longmer probes representing 25,000 genes and about 38,000 gene transcripts. The design is based on the Ensembl Mouse Database release 26.33b.1, Mouse Genome Sequencing Project, NCBI RefSeq, Riken full-length cDNA clone sequence, and other GenBank sequence.21,335 mouse NCBI RefSeq gene transcript sequences are represented; pseudogenes are excluded from oligo design. The design approach allows detection of alternative splicing variants using common, partial common, and individual transcript probes. 16,324 oligos from the Mus musculus (mouse) AROS V3.0 are also used in the Mus musculus (mouse) AROS V4.0. All probes are Tm normalized to 78ºC (±5°C) and have a 5' amino linker.
Externally sourced microarrays used with the BPFG
We have collaboratively supported a range of projects using externally sourced microarray. These have included:
Microarrays from the MRC HGMP
Now closed, the HGMP supplied a range of microarrays to academic groups in the UK. The substantial advantage of these microarray was that they were essentially provided free and with little restriction on use to the users. They were obviously not free to the MRC who were supporting the research community in this field by providing them in this way. We have performed studies using HGMP supplied mouse, rat, and human microarrays, some of which will lead to publication, and others of which have served to generate preliminary data for subsequent projects for the groups we worked with using these arrays.
We do not currently have an alternative source of equivalent microarrays, and are looking to produce current equivalent slides ourselves in 2007.
Arabidopsis microarrays from Dr David Galbraith, University of Arizona.
Working with groups in the Oxford University department of Plant Sciences, we have collaborated, and have ongoing collaborations, on a number of projects using microarrays for Arabidopsis, printed by the Galbraith lab. Further information on these microarrays and their availability is available from their web site.
Maize microarrays
These microarrays were used and sourced through the Oxford University department of Plant Sciences.
Operon Rattus norvegicus (rat) V3.0 and Operon Homo sapiens (human) V4.0.
Currently these arrays are sourced as required directly from Operon.