Neonatal liver niches program T cell tolerance

Single cell data Raw FASTQ data has been deposited in ENA (accession code: PRJEB104713). We ran the 10X CellRanger pipeline with default configuration to process the raw data. The .tar.gz contains standard output of the CellRanger pipeline for all three libraries: GEX (barcode, matrix, features file), VDJ (contigs file) and FB. These data can be directly read into Seurat (in R) or AnnData object (in python) for further downstream analysis. Spatial transcriptomics data The raw 10X Xenium data is provided in one .tar.gz file and the processed data in another. We used the SPARROW pipeline to analise the data, all steps are described in the publication. The output is available in a zarr store.