This is a public repository containing scripts used in the publication:
Arvidsson G, Czarnewski P, Johansson A, Raine A, Imgenberg-Kreuz J, Nordlund J, Nordmark G, Syvänen AC. Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome. Arthritis Rheumatol. 2023 Aug 23. doi: 10.1002/art.42683. Epub ahead of print. PMID: 37610265.
Two files for setting up the analysis conda environment:
conda/environment_pSS.ymlconda/environment_pSS_MacOS.yml
- Clone the repository\
git clone https://github.com/Molmed/pSS_scRNAseq.git
- Create and activate the conda environment\
cd pSS_scRNAseq
conda activate base
conda install -c conda-forge mamba
mamba env create -n env_pSS -f env_pSS_MacOS.yml
conda activate env_pSS
Datasets used in the study:
| Technology | Dataset | Reference | Accession No |
|---|---|---|---|
| 10X scRNAseq 5' v1.1 | Gene expression of B cells from pSS patients | present study | GSE214974 |
| 10X scVDJseq | VDJ sequencing of B cell receptor from pSS patients | present study | 10.17044/scilifelab.21269619 |
| 10X scRNAseq 5' | Gene expression from sorted B cell subtypes | Stewart et al. Frontiers in Immunology 2020 | E-MTAB-9544 |
| PCR product sequencing | IGH CDR3 sequences from pSS patients | Corsiero et al. Plos One 2014 | #### |
| PCR product sequencing | IGH CDR3 sequences from pSS patients | Visser et al. Frontiers in Immunology 2020 | GenBank Accession Numbers: MT151387–MT151600 |
| Protein sequencing of purified RF antibodies | IGH CDR3 sequences from RF antibodies in pSS patients | Wang et al. Arthritis Rheumatol. 2018 | #### |