2023-Inamo et al-preprint

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"Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis"
Jun Inamo, Joshua Keegan, Alec Griffith, Tusharkanti Ghosh, Alice Horisberger, Kaitlyn Howard, John Pulford, Ekaterina Murzin, Brandon Hancock, Anna Helena Jonsson, Jennifer Seifert, Marie L. Feser, Jill M. Norris, Ye Cao, William Apruzzese, S. Louis Bridges, Vivian Bykerk, Susan Goodman, Laura Donlin, Gary S. Firestein, Harris Perlman, Joan M. Bathon, Laura B. Hughes, Darren Tabechian, Andrew Filer, Costantino Pitzalis, Jennifer H. Anolik, Larry Moreland, Joel M. Guthridge, Judith A. James, Michael B. Brenner, Soumya Raychaudhuri, Jeffrey A. Sparks, The Accelerating Medicines Partnership RA/SLE Network, V. Michael Holers, Kevin D. Deane, James A. Lederer, Deepak A. Rao, Fan Zhang
bioRxiv, posted July 04, 2023
https://doi.org/10.1101/2023.07.03.547507

- will update when/if this is peer-reviewed and published

- "Data availability All raw and processed data will be available upon acceptance."

[mleipold]

Now published:

J Clin Invest. 2025, 135, e185217
https://doi.org/10.1172/jci185217

- "Data and code availability. The results published here are in whole or in part based on data obtained from the ARK Portal (http://arkportal.synapse.org). The AMP RA/SLE Network data used for this publication are available at https://doi.org/10.7303/syn64425850.2 and https://arkportal.synapse.org/Explore/D ... d=64425850 The ARK Portal hosts data generated by a network of research teams working collaboratively to deepen the understanding of arthritis and autoimmune and related diseases. It was established by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) and includes data from the AMP RA/SLE program. Values for all data points in graphs are reported in the Supporting Data Values file. All source code to reproduce the analyses is available on GitHub (https://github.com/fanzhanglab/AtRiskRA_SingleCell/). Supplemental material for this paper is available online."

- https://arkportal.synapse.org/Explore/D ... d=64425850
- "Dataset Details: This study profiled gene and protein expression patterns in PBMCs from healthy control, RA, and at-risk RA subjects using CyTOF data from AMP-RA.SLE PhaseII CyTOF corresponding to 167 subjects and CITE-seq data from AMP RA.SLE Phase II PBMC CITE-seq corresponding to 140 subjects. The corresponding files from these two datasets are included here. Publication-specific data includes 16 .Rds files consisting of SeuratObjects and sparse matrices of protein and gene expression and cell-level metadata. Additional clinical metadata is also included. These files can be selected from the dataset by filtering on publicationSynID = ''syn64429482" and are stored under the folder syn64425755."
- this link does contain FCS files, but it's unclear which ones are used for this paper: if you limit to Publication Syn ID "syn64429482" and Data Type "cytometry", there are only 5 RDS files. If you don't limit the Publication Syn ID, it retrieves 1173 FCS files.
- Similarly, there are only RDS files if you follow the Folder link mentioned: https://www.synapse.org/Synapse:syn64425755

- if you follow the "CyTOF data from AMP-RA.SLE PhaseII CyTOF" link, you wind up at "AMP RA.SLE PhaseII CyTOF": https://arkportal.synapse.org/Explore/D ... d=52623570
- this contains 2499 FCS files.