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 Microarrays

Effective July 1, 2008, the BCBC Functional Genomics Core no longer distributes, or provides support for, high density microarrays.

These chips were developed by Dr. Klaus Kaestner's group, in collaboration with Dr. Chris Stoeckert's group, in the Department of Genetics at the University of Pennsylvania, Philadelphia. We are keeping background information below for historical purposes but please be advised that we cannot provide additional support for these other than what is detailed below.

Lastly, please refer to the official news release.


Microarrays

icon Mouse PromoterChip BCBC-5A
The Mouse PromoterChip BCBC-5A represents a significant upgrade to earlier versions of the Mouse PromoterChips, containing over 18,000 proximal and distal promoter regions. Promoter regions were determined from full length cDNA libraries and Reference Sequences (RefSeqs). Over 12,000 well characterized genes were chosen and are represented by either a 1 kb or 2 kb tile, PCR amplified from genomic material. The PromoterChip BCBC-5A is a powerful new tool that can be used for location analysis of global histone modification as well as specific binding by transcription factors. When both the Mouse PromoterChip BCBC-5A and 5B chips are used together, investigators will be able to use these simple techniques to rapidly screen over 35,000 genomic elements.

icon Mouse PromoterChip BCBC-5B
The Mouse PromoterChip BCBC-5B complements the Mouse PromoterChip BCBC-5A and contains over 18,000 elements, the majority of which represent potential regulatory regions such as enhancers, microRNA regions, and highly conserved genomic regions. The BCBC-5B chip also contains an additional 5,100 promoter regions not included on the BCBC-5A chip. Promoter regions were determined from full length cDNA libraries and Reference Sequences (RefSeqs). All regions are represented by a 1 kb tile, PCR amplified from genomic material.

icon Mouse PancChip 6
The Mouse PancChip 6 contains approximately 13,000 mouse cDNAs chosen for their expression in various stages of pancreatic development, many of which are not found on commercially available arrays. Many of these clones where chosen to represent every assembly found to be expressed in the pancreas by sequence analysis of Consortium Libraries EPConClones. In addition, well characterized probes amplified from full-length sequence verified transcripts known to be involved in pancreas development and pathways relating to glucose homeostasis are included. More than 90% of the elements on the Mouse PancChip 6 are also expressed in liver, making this array useful for investigators interested in hepatic metabolism. The high level of homology between mouse and rat genes also makes this array suitable for use with tissues or cells derived from the rat. Note that quality control measures have resulted in sequence verification of 96% of the probes on Mouse PancChip 6.

icon Human PancChip 1
Similar to the Mouse PancChip 6, the Human PancChip 1 contains over 12,000 cDNAs known to be expressed in the pancreas/islets. In addition, well characterized probes amplified from full-length sequence verified transcripts known to be involved in pancreas development and pathways relating to glucose homeostasis are included.

For further details on any of these PancChips, including complete details of spot annotation, please refer to the BCBC-EPConDB website.