processed scRNA-seq data for Neuwirth & Malzl et al. 2024

This dataset contains the analysed scRNA-seq data used in Neuwirth & Malzl et al. 2024 as AnnData objects. You can find the code used to produce and analyse this data on GitHub. All data was preprocessed using cellranger v6.0.1 with GRCh38 3.0.0 as reference.

Psoriasis and Sarcoidosis PBMC data

pbmc.scps.integrated.clustered.h5ad: contains scVI-integrated and Leiden-clustered data of Psoriasis and Sarcoidosis patient blood as well as healthy controls (Psoriasis data was generated within this study; Sarcoidosis data was reprocessed from 10.1016/j.immuni.2023.01.014)tcells.pbmc.scps.integrated.clustered.h5ad: contains scVI-integrated and Leiden-clustered T cell subset of Psoriasis and Sarcoidosis PBMC data

Atopic dermatitis skin data

tissue.ad.integrated.clustered.h5ad: contains scVI-integrated and Leiden-clustered data of healthy and atopic dermatitis patient skin (reprocessed from 10.1126/science.aba6500)tcells.tissue.ad.integrated.clustered.h5ad: contains scVI-integrated and Leiden-clustered T cell subset of atopic dermatitis data

Psoriasis and Sarcoidosis skin data

tissue.scps.integrated.annotated.h5ad: contains scVI-integrated and celltypist-annotated data from Psoriasis and Sarcoidosis patient skin as well as healthy controls (Psoriasis data was reprocessed from 10.1126/science.aba6500; Sarcoidosis data was reprocessed from 10.1016/j.immuni.2023.01.014)tcells.tissue.scps.integrated.clustered.h5ad: contains scVI-integrated and Leiden-clustered T cell subset of Psoriasis and Sarcoidosis skin datatregs.tissue.scps.integrated.annotated.h5ad: contains scVI-integrated and SAT1 status annotated regulatory T cell subset of Psoriasis and Sarcoidosis skin datatregs.tissue.scps.integrated.milo.h5ad: basically same as above but with cell neighborhood overrepresentation analysis on top

IBD colon data

tissue.uc.integrated.clustered.h5ad: contains scVI-integrated and Leiden-clustered data of Crohn's disease and ulcerative colitis patients as well as healthy controls (reprocessed from 10.1126/sciimmunol.abb4432)tcells.tissue.uc.integrated.clustered.h5ad: contains scVI-integrated and Leiden-clustered T cell subset of IBD data

Raw and unfiltered data

inflammatory_disease.h5ad: contains the raw, unfiltered and unprocessed data of all the files above (i.e. combined cellranger output) and is the source data file of all analyses in this study. If you just want the untouched data this is what you want to use.