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Figure 1. Complete work-flow of the Scasat

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1 Figure 1. Complete work-flow of the Scasat
Figure 1. Complete work-flow of the Scasat. The data processing steps consist of the preprocessing steps of trimming low quality bases, aligning the reads with the corresponding genome and calling the peaks. The peak accessibility matrix is then generated by merging all the mapped BAM files of each single cell and calling peaks in this merged file. The downstream analysis is composed of the necessary steps to conduct statistical analysis on the single cell ATAC-seq data. In Scasat the data are converted into a binary dataset. Dimensionality reduction methods are then applied to this binarized data. Other statistical analysis is then performed on this reduced dimension to infer biological information. From: Classifying cells with Scasat, a single-cell ATAC-seq analysis tool Nucleic Acids Res. Published online October 18, doi: /nar/gky950 Nucleic Acids Res | © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

2 Figure 2. Experimental design for disentangling different cell types from a complex mixture. Three cell types HET1A, OE19 and OE33 are mixed in equal proportions. Samples are then taken from this mixture into two independent batches (Batch-1 and Batch-2) by running them in two C1 integrated fluidic circuits (IFC). The captured cells are then sequenced using a NextSeq. From: Classifying cells with Scasat, a single-cell ATAC-seq analysis tool Nucleic Acids Res. Published online October 18, doi: /nar/gky950 Nucleic Acids Res | © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

3 Figure 3. MDS plot with (A) and without (B) additional filtering to remove peaks where very few cells from a specific batch have open peaks. In (A) cells can be separated using only the batch information which is removed in (B) with additional filtering. (C) shows the three clusters identified by k-medoids clustering algorithm. (D) MDS plot derived from the mixed cell dataset using cells from clusters 1–3 (C) and cells from experiments conducted with pure populations of HET1A and OE19. B1 and B2 in OE19 refers to two batches of OE19 single cells. The clusters from the mixed population group with their inferred cell-types. From: Classifying cells with Scasat, a single-cell ATAC-seq analysis tool Nucleic Acids Res. Published online October 18, doi: /nar/gky950 Nucleic Acids Res | © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

4 Figure 4. Correlation plot showing Pearson correlation for the three clusters of cells identified with k-medoid clustering algorithm, against the bulk and two other single-cell data for which the cell types were known a priori. These known single-cell data are for HET1A and OE19 done in two batches (B1 and B2). Single cells from these known cell types are also aggregated. The bulk datasets have the label bulk at the end of the sample name. Here red indicates negative correlation and blue indicates positive correlation (scale bar on the right). From: Classifying cells with Scasat, a single-cell ATAC-seq analysis tool Nucleic Acids Res. Published online October 18, doi: /nar/gky950 Nucleic Acids Res | © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

5 Figure 5. Confirmation of our assignments through visualizing peaks across different genome location from UCSC genome browser track. The clusters in three different colors (red, blue, green single cell clusters) correspond to the inferred aggregated single-cell peak pattern. The bottom three tracks in black show the peaks for the bulk data of OE33, OE19 and HET1A respectively. Peaks around the gene body of (A) GATA6, (B) PPFIA3, (C) CAV1, (D) MAS1 are shown in the figure. For these genes, peaks are more open in (A) and (B) OE19 cells, (C) OE33 and (D) HET1A cells. From: Classifying cells with Scasat, a single-cell ATAC-seq analysis tool Nucleic Acids Res. Published online October 18, doi: /nar/gky950 Nucleic Acids Res | © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

6 Figure 6. Disease ontology from the differentially accessible peaks in Cluster-2 compared to Cluster-3. We identified all the peaks that are differentially accessible in Cluster-2 with a log<sub>2</sub>FoldChange of more than two. We then identified the disease ontologies that are associated with these peaks. Similarly we identified the peaks that are differentially accessible in Cluster-2 compared to Cluster-3 with positive log<sub>2</sub>FoldChange (more open in Cluster-2) and identified the disease ontologies associated with these peaks. We then took the 15 topmost disease terms associated Cluster-2 based on p-values along with esophageal carcinoma as two cell lines are related with esophageal carcinoma. The Binomial p-values for these peaks in both clusters are plotted in the –log<sub>10</sub> scale here. All the diseases that have very high confidence in Cluster-2 are related with cancer. For these same disease, there is much lower statistical significance in Cluster-3. For esophageal carcinoma, the statistical significance is higher in Cluster-2 compared with Cluster-3 further supporting the conclusion that Cluster-2 is mostly composed of OE19 cells and Cluster-3 is mostly composed of HET1A cells. From: Classifying cells with Scasat, a single-cell ATAC-seq analysis tool Nucleic Acids Res. Published online October 18, doi: /nar/gky950 Nucleic Acids Res | © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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