Genomics and Gene Targeting Core

Genomics and Gene Targeting Core - Arrays

Our “PancChip” arrays 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 .

Mouse PancChip 6

The Mouse PancChip 6 was released in April 2005 and contains 13,059 mouse cDNAs chosen for their expression in various stages of pancreatic development, many of which are not found on commercially available arrays. This version of the PancChip represents a significant upgrade to the PancChip 5, with the addition of over 1000 full-length clones of particular importance to the field of pancreatic development and pathways relating to glucose homeostasis, as identified and requested by members of the BCBC and IDOM. Note that stringent quality control measures resulted in the sequence verification of all probes on both the mouse and human PancChips.

Human PancChip 1

The Human PancChip 1 is similar to the Mouse PancChip 6.0, containing 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.

Note that > 90% of the elements on the PancChip are also expressed in liver and colon. The high level of homology between mouse and rat genes also makes the Mouse PancChip arrays suitable for use with tissues or cells derived from the rat.

Mouse PromoterChips BCBC-5A and BCBC-5B

Mouse PromoterChips BCBC-5A and BCBC-5B

The Mouse PromoterChip BCBC-5A and BCBC-5B allow for the rapid screening of over 30,000 promoter regions and regulatory elements using the powerful ChIP-on-Chip assay. The BCBC-5A chip contains 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 BCBC-5B contains over 18,000 potential regulatory regions such as enhancers, microRNA regions, highly conserved genomic regions, and an additional 5,100 promoter regions not included on the BCBC-5A chip. Each of these arrays contain over 18,000 proximal and distal promoter regions. Together these chips provide a powerful new tool that can be used for location analysis of global histone modification as well as specific binding by transcription factors.

Agilent Technologies Long Oligo Arrays

We now offer our clients the option of using Agilent Technologies commercially available arrays. These arrays may be of particular interest to investigators looking at tissues or systems other than the pancreas and liver, such as brain, muscle, fat, kidney, etc. These arrays compete directly with Affymetrix arrays in terms of having genome-wide coverage, but offer greater sensitivity for a lower cost.

Agilent-designed 60-mer oligonucleotide microarrays are processed through a powerful combination of probe design algorithms coupled with Agilent's probe selection process. We can currently offer three Agilent arrays:

Each contains 44,000 elements, with over 41,000 human, mouse or rat transcripts.

MGH Mouse Long-Oligo Array

The MGH mouse oligo chip contains 14,611 70-mer oligos designed to represent known and well characterized genes from all tissues. This array is similar to the Agilent arrays but offers the end user a low cost alternative with fewer genes.

Note: This array is being phased out and is now only available for users requiring 50 or more slides.

Custom Arrays

We will print user supplied oligo or cDNA sets using our expertise in array manufacture and highest QC standards. All arrays are printed using our state of the art NanoPrint™ system, which manufactures high quality, precision microarrays utilizing the ArrayIt brand patented Stealth Micro Spotting Device, superior linear drive motion control technology, and proprietary Warp1 controllers.