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Use single-cell transcriptomics and proteomics to study Rheumatoid Arthritis (RA)

Accelerating Medicines Partnership (AMP) Phase 1


This repo provides the Data availability, Source code, Website for our work on using single-cell transcriptomics and proteomics data to define inflammatory cell states in autoimmune disease - rheumatoid arthritis.

The published paper can be viewed and cited:

Zhang, F., Wei, K., Slowikowski, K., Fonseka, C.Y., Rao, D.A., et al, 2018. Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry. Nature Immunology, 2019.

Data availibility

The raw data of this study are available at:

Database Link with accession code Data type
ImmPort SDY998 single-cell RNA-seq, mass cytometry, bulk RNA-seq, flow cytometry, clinical and histology
dbGAP phs001457.v1.p1 single-cell RNA-seq and mass cytometry

Send us ( or an email if you have any quesitons or requests for data download.

Source code

Clone this repo:

cd ~/work/
git clone
cd amp_phase1_ra


The files in the repo are organized as follows:

├── R
|── data

data/ has Excel sheets with sample metadata and RData files with processed data ready for analysis.

R/ has code for analysis and creating figures:

  • Classify tissue samples using Mahalanobis distance: R/optimal_lymphocyte_threshold.R

  • Integrate bulk with single-cell RNA-seq: R/scRNAseq_bulkRNAseq_integrative_pipeline.R

  • Cluster and disease association test using mass cytometry: R/Tcell.SNE.densVM.server.R, R/Tcell.MASC.R

  • Identify cluster marker genes: R/cluster_marker_table.R, R/limma_differential_bulk.R

  • Functions for PCA, densisty analysis, etc: R/pure_functioins.R

  • Visualize results: R/cytof_results_plot.R, plot_cluster_markers.R, etc

  • More

Send us ( an email if you have any quesitons for the analysis.


Feel free to check out the websites and search your favorite genes:

  1. Shiny app: view single-cell RNA-seq, bulk RNA-seq, and mass cytometry data for rheumatoid arthritis data.
  2. UCSC Cell Browser: view single-cell RNA-seq datasets: 1 rheumatoid arthritis dataset and 2 lupus datasets.
  3. Broad Institue Single Cell Portal: view single-cell RNA-seq datasets: 1 rheumatoid arthritis datset and 2 lupus datasets.

For example, get everyting in one page using Shiny app:


Send us (,, or an email if you have any quesitons.


🌾 Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.





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