Clonally resolved spatial transcriptomics data of mouse spleen
Description
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.
Files
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Additional details
Related works
- Is supplement to
- Preprint: 10.1101/2023.11.21.568179 (DOI)