ATAC-Seq Differential Analyisis

**Table 1.** Number of aligned reads and open bases in each sample. *Factor* is a scaling factor computed based on the number of aligned reads and on the total open bases. *Peaks* is the number of peaks detected in each sample. *FRIP* is the fraction of reads that fall in peaks. According to ENCODE guidelines, this should be over 30%, and definitely not less than 20%.
Sample	Aligned reads	Open bases	Factor	Peaks	FRIP
RC-W-C-1	72,319,686	71,811,473 bp	1.264	89,570	24.4%
RC-W-C-2	67,073,293	52,825,702 bp	1.003	73,766	17.0%
RC-W-C-3	58,153,517	39,729,441 bp	0.870	63,292	15.8%
RC-M-C-1	99,709,791	78,316,596 bp	1.000	91,663	20.1%
RC-M-C-2	92,567,057	70,975,263 bp	0.976	82,606	19.4%
RC-M-C-3	77,736,068	68,480,874 bp	1.122	84,056	18.7%

**Table 2.** WashU genome browser tracks for all samples, and for all conditions.
SAMPLES	CONDITIONS

**Table 3.** Number of comparable peaks and average peak sizes in each contrast.
Test	Ctrl	Number of peaks	Avg size in Test	Avg size in Ctrl
RC-M-C	RC-W-C	81,507	946.7 bp	1301.5 bp

**Table 4.** Differential peaks in each contrast. To determine differential peaks, the peaks in both conditions (test and control) are merged, to form a set of comparable peaks. The number of aligned reads in each alignable peak is then computed for all replicates of the two conditions, to produce a peak size matrix. Finally, this matrix is analyzed with DESeq2 to identify peaks that are significantly higher in the test or in the control condition. The *Significant* column reports the number of comparable peaks showing a significant difference between test and control; the *Up in Test* and Up in Ctrl columns show the number of peaks that are higher in test and in the control condition respectively. The Excel files in the *Full results* column contain the position, fold change, and P-value for all significantly different peaks.
Test	Ctrl	Significant	Up in Test	Up in Ctrl	Full results	WashU hub
RC-M-C	RC-W-C	1,271	871	400	RC-M-C.vs.RC-W-C-diffpeaks.csv	RC-M-C.vs.RC-W-C.json

**Table 5.** Genes showing increased or decreased accessibility at transcription start sites.
Test	Ctrl	Significant	Accessibility		Genes
Test	Ctrl	Significant	Increased	Decreased	Genes
RC-M-C	RC-W-C	1,577	555	1,022	RC-M-C.vs.RC-W-C.TSS.xlsx

**Table 6.** Genes showing increased or decreased accessibility measured across the whole gene body.
Test	Ctrl	Significant	Accessibility		Genes
Test	Ctrl	Significant	Increased	Decreased	Genes
RC-M-C	RC-W-C	1,130	295	835	RC-M-C.vs.RC-W-C.genes.xlsx

**Table 7.** Plots based on contrast data. The plots in the *Peak sizes* column show a scatterplot of the size of common peaks in the Test and Control conditions. Dots above the diagonal indicate that the peak is larger in the Test sample than in the Ctrl sample. *TSS* plots show the ATAC profile around transcription start sites in the Test and Control conditions. *Test Peaks* heatmaps show the profile of peaks that are significantly higher in Test (from Table 3) in both conditions. *Ctrl Peaks* shows the same information for peaks that are higher in the Control condition.
Test	Ctrl	Peak sizes	TSS	Test Peaks	Ctrl Peaks
RC-M-C	RC-W-C	RC-M-C.vs.RC-W-C.scatterplot.png	RC-M-C.vs.RC-W-C.TSS.png	RC-M-C.vs.RC-W-C.testpeaks.png	RC-M-C.vs.RC-W-C.ctrlpeaks.png