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| Status |
Public on Mar 07, 2022 |
| Title |
RNA and surface epitope sequencing of single cells involved in spondyloarthritis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Early diagnosis of psoriatic arthritis (PSA) and differentiation of this disease from similar but distinct arthritides, such as ankylosing spondylitis (AS), is important for successful therapeutic intervention but currently remains challenging due, in part, to the scarcity of non-invasive biomarkers. In this study, we perform single cell profiling of transcriptome and cell surface protein expression on the peripheral blood immunocyte populations of individuals with PSA, individuals with AS, individuals with cutaneous psoriasis (PSO) alone, and healthy individuals to identify gene and protein features differentially expressed between these groups across 30 immune cell types and to further evaluate the diagnostic potential of these features using a machine learning classification approach.
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| Overall design |
RNA and surface epitope sequencing of peripheral blood mononuclear cells in 28 patients with psoriatic arthritis (PSA), 10 patients with ankylosing spondylitis (AS), 24 patients with cutaneous psoriasis only (PSO), 14 psoriasis patients with unclear PSA diagnosis (PSX), and 29 healthy subjects. StudyInfo_20220124.xlsx describes the samples, as well as raw and processed data used for separate studies of (1) AS and healthy subjects and (2) PSA, PSO, PSX, and healthy subjects, as well as a description of the columns in the corresponding CellMetadata files of each study. CellMetadata_AS_20220103.tsv indicates the subset of cells used in the study of AS and healthy subjects. CellMetadata_PSA_20220103.tsv indicates the subset of cells used in the study of PSA, PSO, PSX, and healthy subjects.
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| Contributor(s) |
Liu J, Alber S, Kumar S, Hong J, Huang Z, Paez D, Castillo M, Calvo M, Chang H, Cummins DD, Chung M, Yeroushalmi S, Bartholomew E, Hakimi M, Ye CJ, Bhutani T, Matloubian M, Gensler L, Liao W |
| Citation(s) |
35309349 |
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| Submission date |
Jan 25, 2022 |
| Last update date |
Jul 12, 2022 |
| Contact name |
Wilson Liao |
| E-mail(s) |
wilson.liao@ucsf.edu
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| Organization name |
University of California, San Francisco
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| Department |
Dermatology
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| Street address |
2340 Sutter St.
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (48)
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| Relations |
| BioProject |
PRJNA800261 |
| SRA |
SRP356618 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE194315_CellMetadata-AS_TotalCiteseq_20220711.tsv.gz |
5.4 Mb |
(ftp)(http) |
TSV |
| GSE194315_CellMetadata-PSA_TotalCiteseq_20220103.tsv.gz |
5.6 Mb |
(ftp)(http) |
TSV |
| GSE194315_PBMC-01-07_processed_data_files.tar.gz |
3.0 Gb |
(ftp)(http) |
TAR |
| GSE194315_StudyInfo_20220124.xlsx |
16.9 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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