Exploratory Analysis

This ATAC-seq dataset contains accessibility profiles for 31894 cells.

Signal has been summarized for the following region sets:

Fragment data IS available.

Iterative LSI was used for clustering and for dimension reduction.

Method	umap
Annotation	.ALL .sampleId cellType clusterAssignment nFrags nTotal nPass tssEnrichment PC1 PC2 PC3

Figure 1

Dimension reduction

chromVAR [1] analysis. The following motif set(s) were used for the analysis: jaspar_vert. R data files of chromVAR deviation scores have been attached to this report:

• .peaks.itlsi: RDS file
• .peaks.itlsi: RDS file

Region type

.peaks.itlsi

Figure 2

chromVAR variability. TF motifs are shown ordered according to their variability across the dataset.

Region type	.peaks.itlsi
Motif	MA0036.3_GATA2 MA0652.1_IRF8 MA0154.3_EBF1 MA0800.1_EOMES MA0102.3_CEBPA MA0466.2_CEBPB MA1141.1_FOS_JUND MA0080.4_SPI1 MA0105.4_NFKB1 MA0014.3_PAX5 MA0002.2_RUNX1 MA0690.1_TBX21 MA0769.1_Tcf7

Figure 3

Dimension reduction annotated with chromVAR deviation scores

1. Schep, Wu, Buenrostro, & Greenleaf (2017). chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nature Methods, 14(10), 975-978