H3K27me3 in four squamous cell carcinoma cell lines

ABSTRACT: ChIP-Seq for H3K27 trimethylation was performed for two HPV-positive and two HPV-negative squamous cell carcinoma cell lines. The data served two purposes. First, the data were used as an example implementation of our novel ChIP-Seq Peak Prioritization pipeline, PePr. We have developed the PePr pipeline, a ChIP-Seq Peak Prioritization pipeline that accounts for the variation among replicates and peak location relative to a gene. We show, using a transcription factor dataset (which exhibited small variation among samples), that PePr performs favorably compared to commonly used peak callers and that it achieves balanced sensitivity and specificity. We also show, using histone modification data (which exhibited larger variation among samples), that PePr can improve the detection of different

ORGANISM(S): Homo sapiens

SUBMITTER: Maureen Sartor 

PROVIDER: E-GEOD-38629 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress