The BCBC Functional Genomics Core manufactures and prints in house high density microarrays for distribution at a low cost to researchers throughout the world. 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. Our arrays are printed on Corning ULTRA Gaps slides, giving very low background and high signal to noise ratios. Stringent QA and QC measures are used throughout the entire process and all array print runs are rigorously quality controlled by test hybridization to our standard probes. Stratagene's SpotReport - 10 Array Validation System, and several hundred blank spots are provided as negative controls. Publications resulting from the use of these chips can be found here.


We currently offer four arrays:

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.

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.

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 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.

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.

Figure 1: ChIP-on-Chip

A modification of microarray technology utilizes spotted promoter regions instead of cDNA sequences. After Chromatin Immunoprecipitation with an antiserum raised against a particular transcription factor, the immunoprecipitated DNA is amplified, labeled, and hybridized against these promoter microarrays. Spots that are brighter in the immunoprecipitated channel than the control represent promoter sequences to which the transcription factor is bound. This technique, termed "genome-wide location analysis", or "ChIP-on-Chip" has been utilized to determine binding sites for several transcription factors in yeast, and higher organisms (2005 Le et al, PLoS Genet).

Basic Experimental Guidelines (Kaestner Lab Tested):

• Use >=4 biological replicate samples for each experimental condition tested.
• RNA must be of high quality (determine this using an Agilent Bioanalyzer)
• Use 20ug of total RNA per sample or 2ug of an RNA (typically a 100 ng amplification will yield this)
• Confirm Microarray results using qpcr, northern blots.

Download protocols for labeling cDNA and Hybridizing to the PancChip. Also find here a handbook for preparing suitable RNA for labeling to a microarray

We have a new white paper discussing issues surrounding experimental design.

Figure 2: Chip dimensions

Comprehensive files containing annotations for the chip are provided on the PancChip information page. Detailed information describing the headers for this file are can also be found there in PDF format.

Our chips are printed using a NanoPrint Microarrayer and 48 Telechem Stealth Micro spotting pins (SMP2.5) onto Corning ULTRA GAPS slides, using 50% DMSO as a spotting buffer.

Each chip are composed of 48 grids. The grids are separated by 250 microns in both X and Y dimensions.

Figure 3: Location of Cy3 anchors on PancChip 6.0

Slides can be scanned in several different orientations depending on the type of scanner used. Please see instructions specific for each chip via the Downloads page and in the Chip documentatation. For PromoterChip-5A, Mouse PancChip 6.0, Human PancChip 1.1, and PromoterChip-3.1 the result of a scan should produce an image with the Cy3 anchors in the bottom right corner of the array as shown in Figure 3. However, for the earlier versions of our arrays, Mouse PancChip 5.0 and Human PancChip 1.0, the result of a scan should produce an image with the Cy3 anchors in the top right corner of the array.

Figure 3, shows an image of PancChip 6.0, in which feature 1.1.1.1.1.1 is the top left spot in the top left grid when viewed in this orientation. See Feature Location description in the documentation file for further explanation of Feature Location.

We have provided input files for several image analysis applications on the PancChip spotting information page. If your software application is not listed and you would like to provide a file for other users, please contact EPConDB@pcbi.upenn.edu.