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 reference
  profiles 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 results
  were 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, including
  separate assays for "sender" and "receiver" signals

gene metadata

• logical flags indicating wether or not
  features 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)