Supplement to: A transcriptional map of human tonsil architecture

Flat files & results. metadata.csv captures section-level information, namely did/sid - slide (S1, S2) & section identifier (C1, A1, A2)(slide S1: sections C1 and A1, slide S2: section A2) min/max - field of view (FOV) correspondence S1/S2.zip archives contain flat files for each slide, namely, the following set of .csv.gz files: positions - field of view (FOV) placement polygons - cell segmentation boundaries counts - (genes x cells) count matrix transcripts - single-molecule data metadata - cell-level metadata ref.zip contains scRNA-seq data-derived referenceprofiles used for InSituType clustering, namely: mtx.rds - derived from low-res. annotations mty-sub.rds (where sub = bcs/epi/mye/str/tcs) - derived from subset-wise high-res. annotations for each section (C1, A1, A2), analysis resultswere collected & written to following formats .rds files contain SingleCellExperiment objects (R) .h5ad files contain AnnData objects (Python) .zip archives contain alabaster file artifacts metadata thresholds employed during quality control n - total RNA counts m - uniquely detected RNAs a - area-normalized RNA counts d - distance to FOV border (um) alternative experiments Negative - quantify non-specific ISH probe hybridization SystemControl - quantify misidentification of reporter readout COMMOT - cell-cell communication scores, includingseparate assays for "sender" and "receiver" signals gene metadata logical flags indicating wether or notfeatures were used for clustering all = used for ist/lv1 (low-resolution clustering) bcs/epi/mye/str/tcs = used for jst/lv2 (high-res.) cell metadata fil - indicates if a cell passed quality control epi/gcs - annotation of epithelial (EPI00) & germinal center (GC00) substructures i/jst - low-/high-resolution cluster assignments lv1/2 - low-/high-res. cluster annotations cty - niche annotations (e.g., TCZ)