Single-cell spatial transcriptomic data of synovial tissue from Rheumatoid Arthritis (RA) patients in active disease and sustained clinical remission.

ABSTRACT: We used the Nanostring CosMx Spatial Molecular Imaging platform to measure expression of 960 genes discriminating transcriptional profiles and spatial localization of 127,199 cells (69 fields-of-view (FOV)) in paraffin-embedded synovial biopsies from 3 active and 3 remission RA patients (~11 FOV per donor). Cell Segmentation. Initial image segmentation was performed with Mesmer6189 with the following parameters: mesmer_mode = “both”, scale = pixel size of the images. We used the cell boundaries estimated by Mesmer as a prior for refinement of the segmentation with Baysor6290 based on transcript densities, using the R wrapper (https://github.com/korsunskylab/baysorrr). Following successful cell assignment, we generated a gene-cell expression matrix and performed quality control, removing an

ORGANISM(S): Homo sapiens (human)

SUBMITTER:  

PROVIDER: S-BSST1483 | biostudies-other |

REPOSITORIES: biostudies-other