Single-cell Profiling Reveals Diverse γδ T Cell Subsets in Ulcerative Colitis

Lena S. Mayer, Jakob Arnold, Felix Roettele, Nadine Reuter, Ajinkya Pattekar, Takuya Ohtani, Mariana M. Ribeiro, Rebecca Siwicki, Kerstin Bruder, David Obwegs, Elin Stahl, Sarah Buechel, Natascha Roehlen, Julia Kolter, Zohreh Mansoori Moghadam, Ahmed Alaswad, Zhibek Zhumalidova, Guang Li, Xinjuan Liu, Yang Li, Amit Singh, Jose Villacorta Hidalgo, Maria D. Paraskevopoulou, Vijay Yajnik, Julius Juarez, Yue Ren, Hongzhe Li, E. John Wherry, James D. Lewis, Gary D. Wu, Meenakshi Bewtra, Vesselin T. Tomov, Robert Thimme, Bertram Bengsch, Peter Hasselblatt, Simone Picelli, Maike Hofmann, Sagar This repository contains the code, raw files, and processed datasets needed to reproduce the scRNA-seq and FACS figures in our manuscript. The code is also available on GitHub. Additionally, processed datasets are available on GEO GSE316069 Overview of Figures and Related Files All processing and figure scripts can be found in processing_and_figures_scripts.zip. Unprocessed raw data (count matrices, TCR contigs, FACS files) are either deposited here or can be found in the respective publication's repository: Data related to Smillie et. al, 2019 can be found here SCP259, and data related to Thomas et. al, 2024 are deposited here zenodo (cd8tcells_final.h5ad, epicolonic_final.h5ad). Processed objects to recreate the following figures are provided as R object files (.Rds). Fig. 1, Fig. 3, Fig.4, Fig. S1, Fig.S3, Fig.S4: FLASHseq_processing.R, FLASHseq_figures.R, FLASHseq_gd.Rds, FLASHseq_pySCENIC_auc.csv, FLASHseq_raw_data.zip Fig. 5, Fig. S5: imc_zonation.ipynb (only contains function for the zonation of IMC data) Fig.6, Fig. S6: integrated_L21_Smillie19_processing.R, Smillie19_processing.R, integrated_L21_Smillie19_figures.R, integrated_L21_Smillie19_enterocytes.Rds, integrated_L21_Smillie19_gdTcells.Rds, Smillie_PB.Rds, Li2021_raw_data.zip Fig. 7: Thomas24_processing.R, Thomas_24_figures.R, thomas24_entero_pb.Rds, thomas24_gd_pb.Rds Fig. 8, Fig. S8: PBMC_scRNAseq_processing.R, PBMC_FACS_processing.R, PBMC_figures.R, PBMC_scRNAseq_Vd1.Rds, PBMC_scRNAseq_Vd2.Rds, PBMC_FACS_vd1.Rds, PBMC_scRNAseq_raw_data.zip, PBMC_FACS_raw_data.zip