Single sample snRNA-seq dataset (single nucleus RNA sequencing) from the Precision Cardiology Lab at the Broad Institute.

The sample contains cells from primary tissue from Wistar rat left atrium.  Healthy male rat, 17 weeks old.

This dataset is part of a larger study (manuscript in preparation). This dataset is released here separately because it was analyzed as part of the CellBender paper in published in Nature Methods (2023), as a demonstration of cell calling.

This sample was run using 10x Chromium, and the library preparation used 10x 3' v2 chemistry.

The data shown here in the “Explore” tab is the counts after removing background noise with CellBender.

The QC'ed dataset is available for download in AnnData format in the “Download” tab as “PCL_rat6k_QCed_clustered_SCP.h5ad”.

CellBender paper specifics:

• The cells (nuclei) shown in this study (under the “Explore”) tab are all cells called by any cell calling method, after cell QC.
• CellBender called all the cells shown, as it called the union of all cells called by other methods plus extra cells.
• Cells called by each method (other than CellBender, which called all cells shown) can be visualized using the “cells_<cell-caller>” annotations (e.g. “cells_dropkick”).
• The raw data file used as input to CellBender and the other cell-calling methods (direct from CellRanger v3, before cell calling or cell QC) is accessible in the “Download” tab as “PCL_rat_A_LA6_raw_feature_bc_matrix.h5”.