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Single-cell ATAC-seq output example

The PBMC5k example shows per-cell footprint signatures across B cells, monocytes, and T/NK cells.

To run a small, complete example yourself, follow the PBMC chromosome-22 tutorial. That 300-cell subset teaches the workflow; the figures here use the larger PBMC5k dataset and will differ.

Use the heatmap to compare motif signatures across cell groups. In the UMAPs, each panel places the same cells at the same coordinates; the colors show either cell labels or the selected motif's signature score. Similar colors within a group indicate a shared pattern of signal.

Signature heatmap

Per-cell PBMC5k footprint-signature heatmap grouped into B-cell, monocyte, and T/NK-cell blocks
Per-cell footprint-signature heatmap. Columns are cells grouped by broad cell type; rows are motif signatures.

Eight marker UMAPs

PBMC5k broad-cell-type UMAP and footprint-signature UMAPs for STAT6, FOSB, CEBPA, IRF8, RELA, ZNF683, NR4A1, and SMAD3
Broad cell-type annotation and per-cell footprint-signature UMAPs for STAT6, FOSB, CEBPA, IRF8, RELA, ZNF683, NR4A1, and SMAD3.

Select either figure to open the full-resolution image. The Single-cell workflow describes the commands used to produce these outputs.

The signatures are smoothed using neighboring cells to reduce sparse signal. They describe relative motif-associated patterns, not direct measurements of TF binding in individual cells.