Affymetrix Tiling Arrays
The MCF users interested in ChIP-on-chip processing will need to provide their own sample quality control.
This new product from Zymo may help with DNA purification: http://www.zymoresearch.com/products/dna/chip_dna_clean_up.asp
Also Affymetrix has several suggestions to ensure high sample quality:
Please be aware that the MCF must see your QPCR data from your samples and positive control from both the post-ChIP processing as well as post-amplification. We cannot pass your SAQC Request without the data. If you did not run a positive control, you (or your PI if you are not the PI) will need to sign-off on your samples. The sign-off releases the MCF from any responsibility of inadequate sample or chip performance.
Affymetrix has seen good success rates with polyclonal antibodies but does note batch-to-batch variation. The company recommends Abcam for ChIP-grade antibodies. If a commercial antibody is not available, Affymetrix suggests one of the following for testing specificity: using different peptides in an ELISA assay, peptide blocking with western blot, or an RNAi knockdown of target protein.
After IP, specificity should be tested by selection of known positive and negative sequences with RT-PCR.
Affymetrix recommends a minimum of 10x antibody enrichment factor. User should use 1-10ug anitbody per ChIP (25ug chromatin) and make sure that signal to background ratio is good. Pre-couple the antibody to beads and then use up to 15ug antibody.
The MCF requires users to perform all processing up to but not including amplified sample fragmentation.
These arrays are available for ChIP-on-chip processing but are not presently stocked by the MCF.
* Please contact the MCF for additional restrictions on purchasing non-stock arrays.
| Human Tiling/Promoter Arrays | |
|---|---|
| Human Tiling 1.0R Array Set | $250/array* |
| Human Tiling 2.0R A Array | $425/array* |
| Human Tiling 2.0R B Array | $425/array* |
| Human Tiling 2.0R C Array | $425/array* |
| Human Tiling 2.0R D Array | $425/array* |
| Human Tiling 2.0R F Array | $425/array* |
| Human Tiling 2.0R G Array | $425/array* |
| Human Tiling 2.0R Array Set | $250/array* |
| Human Promoter 1.0R Array | $400/array* |
| Human Chromosome 21/22 2.0R | $400/array* |
| GeneChip ENCODE 2.0R Array | $400/array* |
| Mouse Tiling/Promoter Arrays | |
| Mouse Tiling 1.1R Array Set | $250/array* |
| Mouse Tiling 2.0R A Array | $425/array* |
| Mouse Tiling 2.0R B Array | $425/array* |
| Mouse Tiling 2.0R C Array | $425/array* |
| Mouse Tiling 2.0R D Array | $425/array* |
| Mouse Tiling 2.0R E Array | $425/array* |
| Mouse Tiling 2.0R F Array | $425/array* |
| Mouse Tiling 2.0R G Array | $425/array* |
| Mouse Tiling 2.0R Array Set | $250/array* |
| Mouse Promoter 1.0R Array | $400/array* |