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. Author manuscript; available in PMC: 2018 May 9.
Published in final edited form as: Nat Methods. 2018 Apr 27;15(5):304–305. doi: 10.1038/nmeth.4663

Figure 1.

Figure 1

ATAC Primer Tool enables targeted and allele-specific quantification by ATAC-qPCR. (a) Workflow for primer design and identification of normalization controls using APT and applications of ATAC-qPCR. (b) Illustration of the APT algorithm for identifying optimal ATAC-qPCR primers. Peaks of interest are binned into overlapping windows, and the correlation between the number of spanning fragments and peak height is calculated for each window. Windows with adequate spanning fragments (blue) are selected for primer design. (c) ATAC-PCR of allele-specific accessibility at the TERT promoter. Sequencing of genomic DNA and ATAC-PCR is shown for SNU-423 (top; heterozygous for −124 C>T TERT promoter mutation) and SNU-449 (bottom; wild-type TERT promoter).