Additional file 4 of Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei
datasetposted on 2022-03-17, 04:30 authored by Hao Zhang, Michael E. Rice, Joseph W. Alvin, Dominique Farrera-Gaffney, James J. Galligan, Michael D. L. Johnson, Darren A. Cusanovich
Additional file 4: Supplementary Table S4. Hypergeometric tests. Column 1 (“TF”) indicates the name and source, if provided, of transcription factors. Columns 2 and 3 show the p value and adjusted p value calculated by Benjamini & Hochberg method. Column 4 indicates the fold enrichment. Column 5 shows the number of condition-specific “missing” peaks overlapping with each ChIP-seq data. Column 6 shows the number of “missing” ATAC-seq peaks in each condition. Column 7 indicates the number of background peaks overlapping with each ChIP-seq data. Column 8 shows the total number of background peaks for either native or fixed samples. Column 9 shows the number of ChIP-seq peaks. Columns 10-13 indicate the fixation state, buffer, temperature, and Tn5 enzyme, respectively. The “missing” ATAC-seq peaks were defined as the peaks that were observed in at least three other conditions, but not observed in the condition of interest. The background peaks indicate the peaks shared among at least three conditions and calculated separately for native and fixed samples. The fold enrichment for overlap with each ChIP-seq dataset was calculated by dividing the frequency of ATAC-seq peaks overlapped by ChIP-seq peaks observed in each condition (the ratio of Column 5 to Column 6) by the frequency of ATAC-seq peaks overlapped by ChIP-seq peaks observed in the background peak set (the ratio of Column 7 to Column 8).