Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

95 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

10x single cell gene expression and V(D)J immune profiling of T cells from the blood, synovial fluid and synovial tissue in psoriatic arthritis patients

ABSTRACT: This study shows the pronounced expansion of CD8 T cell clones at sites of active inflammation within the joints of psoriatic arthritis (PsA) patients compared to blood, and characterises the gene expression of expanded clones using droplet based single cell RNA sequencing. Mononuclear cells were separated from freshly acquired paired peripheral blood and synovial fluid samples from 3 PsA patients using density gradient separation, then enriched for CD4 and CD8 T cells using FACS. Additionally, CD45+ leukocytes were enriched by FACS from the cryopreserved synovial tissue of 2 further PsA patients. All cells were then processed using a 10x Chromium Controller and sequenced by Illumina HiSeq 4000 (peripheral blood / synovial fluid) or NovaSeq with S2 flowcell (synovial tissue).

INSTRUMENT(S): Illumina HiSeq 4000, Illumina NovaSeq 6000, NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Frank Penkava

PROVIDER: E-MTAB-9492 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNAseq of ankylosing spondylitis lymphocytes from peripheral blood and synovial fluid

Project description:Single-cell transcriptome of >55,000 cells multiplexed into 4 channels obtained from peripheral blood and synovial fluid of two patients with HLA-B27+ ankylosing spondylitis,.

2021-10-18 | E-MTAB-10948 | biostudies-arrayexpress

Proteinases in psoriatic arthritis

Project description:Characterize active synovial fluid (SF) serine proteinases in psoriatic arthritis (PsA) in comparison to osteoarthritis (OA) and rheumatoid arthritis (RA)

2021-03-29 | PXD022442 | Pride

scRNA-seq with paired V(D)J sequencing of synovial B cells from rheumatoid arthritis patients

Project description:scRNA-seq with paired V(D)J sequencing of synovial B cells from rheumatoid arthritis patients.

2023-08-01 | E-MTAB-12833 | biostudies-arrayexpress

Discovery and Confirmation of a Protein Biomarker Panel with Potential to Predict Response to Biologic Therapy in Psoriatic Arthritis

Project description:An integrated discovery to targeted proteomics approach was used to investigate the protein profiles of good and non–responders to anti-TNF-alpha and T-cell inhibitor treatments in PsA patients. Reverse phase liquid chromatography coupled to tandem mass spectrometry was used to generate protein profiles of synovial tissue obtained at baseline from 10 PsA patients who then commenced anti-TNF-alpha therapy (adalimumab). Targeted proteomics using multiple reaction monitoring was used to confirm and pre-validate a potential protein biomarker panel in 18 and 7 PsA patient samples respectively.

2019-12-17 | PXD000707 | Pride

Context-specific regulation of monocyte surface IL7R expression and soluble receptor secretion by a common autoimmune risk allele

Project description:IL-7 is a key factor in T-cell immunity and IL7R polymorphisms are implicated in autoimmune pathogenesis. IL7R mRNA is induced in stimulated monocytes in a genetically determined manner. Here we show monocyte surface and soluble IL7R (sIL7R) protein are markedly expressed in response to lipopolysaccharide (LPS). Flow cytometry of synovial fluid-derived monocytes from patients with spondyloarthritis showed an enlarged subset of IL7R+ monocytes. Single-cell RNA sequencing of ex-vivo derived monocytes from the synovial fluid and blood of patients revealed that IL7R+ monocytes at the inflammatory site have a unique transcriptional profile that markedly overlaps that induced by IL-7 in-vitro and shows similarity to the previously described ‘Mono4’ subset. These data demonstrate disease-associated genetic variants at IL7R specifically impact monocyte surface IL7R and sIL7R following innate immune stimulation, suggesting a previously unappreciated key role for monocytes in IL-7 pathway biology and IL7R-associated diseases.

2019-08-12 | E-MTAB-8207 | biostudies-arrayexpress

Single RNA-Seq of synovial tissue macrophages from Rheumatoid Arthritis patients with active disease and in disease remission.

Project description:Treatment refractory Rheumatoid Arthritis (RA) is a major clinical challenge. Drug-free remission is uncommon but provides proof-of-concept that articular immune-homeostasis can be reinstated. In this project, we used single-cell RNA- to study the role of synovial tissue macrophages in maintaining disease remission. We have sequenced synovial tissue macrophages from individuals with healthy synovium (as evaluated by MRI), patients with undifferentiated arthritis (UPA), RA patients naïve to treatment, RA patients resistant to treatment and RA patients in disease remission

2020-04-18 | E-MTAB-8322 | biostudies-arrayexpress

Single cell RNA-sequencing of the human synovium in inflammatory arthritis

Project description:The study presents: - an optimized synovium dissociation protocol for single cell RNA-sequencing studies of the human synovium. The protocol enables the isolation of high yield of viable synovial cells from prospectively collected fresh synovial biopsies from patients with inflammatory arthritis with a minimal sample droupout. The protocol is derived from the method for dissociation of cryopreserved synovia published by Donlin and colleagues (Arthritis Res. Ther. 2019). - a reference single-cell atlas of fresh human synovium in inflammatory arthritis, comprising more than 100´000 unsorted synovial scRNA-seq profiles from 27 freshly dissociated synovia of patients with different types of inflammatory arthritis. The synovial cells segregate into ten lymphoid, 14 myeloid and 17 stromal synovial cell populations and subpopulations, including synovial neutrophils, representing broadly representing the cellular heterogeneity and composition of the human synovium in inflammatory arthritis.

2024-04-21 | E-MTAB-11791 | biostudies-arrayexpress

Microarray analysis of gene expression differences in prostate specific antigen negative (PSA-ve) cells versus PSA+ve cells in LAPC9 and LNCaP prostate cancer (PCa) cells

Project description:Prostate cancer (PCa) is heterogeneous containing both phenotypically differentiated and undifferentiated tumor cells. An important unanswered question is whether these two populations of PCa cells are functionally different. Here we report the distinct molecular, cellular, and tumor-propagating properties of PCa cells that express high (i.e., PSA+) and low (PSA-/lo) levels of the differentiation marker PSA (prostatespecific antigen). PSA-/lo PCa cells are quiescent and resistant to multiple stresses including androgen deprivation, exhibit high clonogenic potential, and possess long-term tumor-propagating capacity in male mice. They preferentially express stem cell-associated genes and can undergo asymmetric cell division generating PSA+ cells. Importantly, PSA-/lo PCa cells can initiate robust tumor development in castrated hosts, survive androgen deprivation, and harbor highly tumorigenic castration-resistant PCa cells that can be further enriched using the ALDH+CD44+α2β1+ phenotype. In contrast, PSA+ PCa cells possess more limited tumor-propagating capacity, mainly undergo symmetric division, and are sensitive to castration. Together, our study suggests that PSA-/lo and PSA+ PCa cells are functionally distinct and PSA-/lo cells may represent one critical source of castration-resistant PCa cells. There are two sets of samples in this study corresponding to two different prostate cancer cell lines LNCaP and LAPC9. Both LNCaP and LAPC9 sets include 3 technical triplicates each that were performed onvdual color arrays and each individual array includes comparison between PSA- (Cy5) and PSA+ (Cy3) cells of the respective cell line.

2012-05-09 | E-GEOD-30114 | biostudies-arrayexpress

The PSA-/lo prostate cancer cells harbor self-renewing long-term tumor-propagating cells that resist castration

Project description:This SuperSeries is composed of the following subset Series: GSE30114: Microarray analysis of gene expression differences in prostate specific antigen negative (PSA-ve) cells versus PSA+ve cells in LAPC9 and LNCaP prostate cancer (PCa) cells GSE35733: Microarray analysis of gene expression differences in prostate specific antigen negative (PSA-ve) cells versus PSA+ve cells in human prostate cancer (HPCa) samples Refer to individual Series

2012-05-09 | E-GEOD-35814 | biostudies-arrayexpress

Illumina HumanmethylationEPIC array analysis in early synovial fibroblasts of RA patients before diagnosis

Project description:In the current study, we compared DNA methylation patterns using the Illumina 850k array technology between normal synovial fibroblasts and synovial fibroblasts from early (veRASF) and late stages of RA (estRASF) and transient, resolving arthritis (rSF). In doing so, we obtained a detailed view of changes in DNA methylation that occur during the development of RA from the earliest clinically apparent stages to established RA with its typical signs and symptoms.

2018-03-31 | E-MTAB-6582 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data