Welcome

This site provides a view of some of the data from the Accelerating Medicines Partnership (AMP) Rheumatoid Arthritis (RA) Phase I project. Here, you can view single-cell RNA-seq, bulk RNA-seq, and mass cytometry data.

Read the paper

Please cite our paper if you use this data in your work:

Defining Inflammatory Cell States in Rheumatoid Arthritis Joint Synovial Tissues by Integrating Single-cell Transcriptomics and Mass Cytometry

Fan Zhang, Kevin Wei, Kamil Slowikowski, Chamith Y. Fonseka, Deepak A. Rao, Stephen Kelly, Susan M. Goodman, Darren Tabechian, Laura B. Hughes, Karen Salomon-Escoto, Gerald F. M. Watts, William Apruzzese, David J. Lieb, David L. Boyle, Arthur M. Mandelin II, Accelerating Medicines Partnership: RA Phase 1, AMP RA/SLE, Brendan F. Boyce, Edward DiCarlo, Ellen M. Gravallese, Peter K. Gregersen, Larry Moreland, Gary S. Firestein, Nir Hacohen, Chad Nusbaum, James A. Lederer, Harris Perlman, Costantino Pitzalis, Andrew Filer, V. Michael Holers, Vivian P. Bykerk, Laura T. Donlin, Jennifer H. Anolik, Michael B. Brenner, Soumya Raychaudhuri

DOI: 10.1101/351130

Overview of synovial tissue workflow

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Contact us

Please contact us if you have any questions or comments on the analysis and results.

Single-cell RNA-seq, bulk RNA-seq, and mass cytometry data



Bulk RNA-seq


Cluster annotations

Fibroblasts (CD45- Podoplanin+)

  • SC-F1: CD34+ sublining fibroblasts
  • SC-F2: HLA+ sublining fibroblasts
  • SC-F3: DKK3+ sublining fibroblasts
  • SC-F4: CD55+ lining fibroblasts

Monocytes (CD45+ CD14+)

  • SC-M1: IL1B+ pro-inflammatory monocytes
  • SC-M2: NUPR1+ monocytes
  • SC-M3: C1QA+ monocytes
  • SC-M4: IFN-activated monocytes

T cells (CD45+ CD3+)

  • SC-T1: CCR7+ CD4+ T cells
  • SC-T2: FOXP3+ Tregs
  • SC-T3: PD-1+ Tph/Tfh
  • SC-T4: GZMK+ CD8+ T cells
  • SC-T5: GNLY+ GZMB+ CTLs
  • SC-T6: GZMK+/GZMB+ T cells

B cells (CD45+ CD3- CD19+)

  • SC-B1: IGHD+ CD270 naive B cells
  • SC-B2: IGHG3+ CD27- memory B cells
  • SC-B3: autoimmune-associated cells (ABC)
  • SC-B4: Plasmablasts