MeDIP was performed using a previously published protocol20 (link), but we also included a ligation-mediated PCR (LM-PCR) step43 (link) to amplify the material (the LM-PCR step was not performed for MeDIP-seq). Hybridizations of pre- and post-LM-PCR samples on custom tile-path arrays (2kb resolution) for the human Major Histocompatibility Complex (MHC) showed that the LM-PCR did not introduce significant bias (Supplementary Fig. 1 online). A detailed protocol is provided in the Supplementary Methods online.
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Protocol for MeDIP with LM-PCR
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Corresponding Organization :
Other organizations : Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Wellcome Trust, Queen Mary University of London, Wellcome Sanger Institute, European Bioinformatics Institute, University College London
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- Inclusion of a ligation-mediated PCR (LM-PCR) step to amplify the material
- Hybridization results on custom tile-path arrays (2kb resolution) for the human Major Histocompatibility Complex (MHC)
- MeDIP protocol used a previously published protocol (20)
- LM-PCR step was not performed for MeDIP-seq
- Positive control: Pre- and post-LM-PCR samples hybridized on custom tile-path arrays to assess if LM-PCR introduced significant bias
- Negative control: Not explicitly mentioned
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