Clonally resolved spatial transcriptomics data of mouse spleen

The BGI Stereo-seq strategy was applied to a mouse spleen sample containing SPLINTR barcoded AML cells.

Data generated with https://github.com/DaneVass/bartools_manuscript_code/blob/main/spatial-analysis/data_preprocessing_m4_paper.py.

mouse4_bin*_bc_counts.tsv:Binned barcode counts across whole slide.Can be merged with AnnData file by `cell_id`.Contains all barcodes detected in a bin (`barcode`) and UMI counts summed by bin (`count_binned`).`isin_adata` marks whether the bin is on the manually segmented tissue section.

mouse4_bin*_bc_counts_top1.tsv:Binned barcode counts on tissue section, barcode with most UMI per bin is selected. 

mouse4_bin*_bc.h5ad:Binned stereo-seq data with barcode information.

mouse4_bin*_bc_clustered.h5ad:Filtered, log1p transformed, scaled, clustered stereo-seq data.Data is not zero centered for bin10 for memory efficiency.