Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of synovial biopsies from rheumatoid arthritis patients

ABSTRACT: Synovial biopsies from rheumatoid arthritis patients were obtained and profiled using RNA-seq. Patients were stratified according to the number of swollen joints they had (SJC, swollen joint count) and divided in three groups for the differential expression analysis: None (SJC = 0), Low (1<= SJC <= 8), High (SJC > 8).

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Homo sapiens

SUBMITTER: Enrico Ferrero

PROVIDER: E-MTAB-6684 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Bisulfite-seq of synovial biopsies from rheumatoid arthritis patients

Project description:Synovial biopsies from rheumatoid arthritis patients were obtained and profiled using bisulfite-seq for whole-genome DNA methylation. Patients were stratified according to the number of swollen joints they had (SJC, swollen joint count) and divided in three groups for the differential expression analysis: None (SJC = 0), Low (1<= SJC <= 8), High (SJC > 8).

2021-04-26 | E-MTAB-6638 | biostudies-arrayexpress

MicroRNA expression profile in macrophages from rheumatoid arthritis and osteoarthritis patients

Project description:In osteoarthritis (OA) and rheumatoid arthritis (RA), many pathological alterations result from aberrant macrophage hyperactivation in the inflamed synovial membrane, and inhibition of macrophage effector functions is a therapeutic strategy in both diseases. Little is known, about the specific genetic circuits that are differentially deregulated in RA and OA macrophages. microRNA (miR) are short single stranded non-coding RNAs involved in the post-transcriptional regulation of gene expression. Altered expression of miRs has been described under various pathological conditions, including rheumatic and other autoimmune diseases. Here we compared the miR expression profile in macrophages isolated from OA and RA patients miR expression in OA and RA macrophages was analyzed using Exiqon miRCURY microarrays. Three biological replicates (patients) were analyzed. Two samples (RA vs OA) were hybridized per microarray.

2016-02-05 | E-GEOD-63745 | biostudies-arrayexpress

Plasma proteomics in children with new-onset type 1 diabetes: a strong tool to identify partial remission biomarkers

Project description:Partial remission (PR) occurs in only half of patients with new-onset type 1 diabetes (T1D) and correspond to a transient period characterized by low daily insulin needs, low glycemic fluctuations and increased endogenous insulin secretion. While identification of newly-onset T1D patients with significant residual beta-cell function may foster patient-specific interventions, reliable predictive biomarkers of PR occurrence currently lack. We analyzed the plasma of children with new-onset T1D to identify biomarkers present at diagnosis that predicted PR at 3 months post-diagnosis. We first performed an extensive shotgun proteomic analysis using Liquid Chromatography-Tandem-Mass-Spectrometry (LCMS/MS) on the plasma of 16 children with new-onset T1D and quantified nearly 1500 unique proteins with 98 significantly correlating with Insulin-Dose Adjusted glycated hemoglobin A1c score (IDAA1C). We next applied a series of both qualitative and statistical filters that yielded to the selection of 26 protein candidates that were associated to pathophysiological mechanisms related to T1D. Finally, we translationally validated several of the candidates using single-shot targeted proteomic (PRM method) on raw plasma. Taken together, we identified plasmatic biomarkers present at diagnosis that may predict the occurrence of PR in a single mass-spectrometry run. We believe that the identification of new predictive biomarkers of PR and β-cell function is key to stratify patients with new-onset T1D for β-cell preservation therapies

2024-04-05 | PXD049795 | Pride

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer

Project description:This SuperSeries is composed of the following subset Series: GSE25083: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: normal head and neck tissue GSE25089: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: HNSCC GSE25091: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: blood controls Refer to individual Series

2011-10-27 | E-GEOD-25093 | biostudies-arrayexpress

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: normal head and neck tissue

Project description:Genome-wide DNA methylation profiling of head and neck squamous cell carcinomas. The Illumina Infinium 27k Human DNA methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in fresh-frozen tumor tissues. Samples included 91 tumors from the oralpharynx and larynx, reflecting all stages of disease, 18 normal head and neck National Disease Research Interchange (NDRI) samples, and 213 normal control blood samples. Bisulphite-converted DNA from the 18 normal head and neck samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

2011-10-27 | E-GEOD-25083 | biostudies-arrayexpress

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: HNSCC

Project description:Genome-wide DNA methylation profiling of head and neck squamous cell carcinomas (HNSCCs). The Illumina Infinium 27k Human DNA methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in fresh-frozen tumor tissues. Samples included 91 tumors from the oralpharynx and larynx, reflecting all stages of disease, 18 normal head and neck National Disease Research Interchange (NDRI) samples, and 213 normal control blood samples. Bisulphite-converted DNA from the 91 head and neck squamous cell carcinoma samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

2011-10-27 | E-GEOD-25089 | biostudies-arrayexpress

Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: blood controls

Project description:Genome-wide DNA methylation profiling of head and neck squamous cell carcinomas (HNSCCs). The Illumina Infinium 27k Human DNA methylation BeadChip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in fresh-frozen tumor tissues. Samples included 91 tumors from the oralpharynx and larynx, reflecting all stages of disease, 18 normal head and neck National Disease Research Interchange (NDRI) samples, and 213 normal control blood samples. Bisulphite-converted DNA from the 213 control blood samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2.

2011-10-27 | E-GEOD-25091 | biostudies-arrayexpress

Proteomic investigation on Anopheles gambiae in Burkina Faso related to insecticide pressures from different climatic regions

Project description:In Sub-Saharan Africa, Anopheles gambiae Giles (Diptera: Culicidae) largely contributes to malaria transmission, in direct relation to environmental conditions influencing the vector ecology. Therefore, our study aimed to compare the proteomes of An. gambiae according to varying insecticide pressures associated to cotton crops also integrating different population origins from two climatic regions of Burkina Faso.

2020-03-09 | PXD016300 | Pride

The screening of cross-reactive targets of recombinant anti-collagen antibody R69-4

Project description:Rheumatoid arthritis (RA) is an autoimmune disease affecting approximately 0.5% of the global population. Despite its prevalence, there is no known cure, underscoring the persistent need for novel therapeutic strategies. In previous studies, we identified a specific subset of antibodies that target an epitope (F4) on type-II collagen (COL2), which seemed to offer protection against arthritis. Leveraging these findings, we have engineered a range of recombinant antibodies against this epitope. Notably, one such antibody, R69-4, has shown significant potential in suppressing arthritis. Here, we aim to identify potential cross-reactive targets of R69-4 to better understand its mechanism of action.

2023-09-05 | PXD044700 | Pride

miRNA profiling in adult rat cardiomyocytes and myocyte-derived progenitor cells

Project description:TLDA miRNA profiling on purified rat cardiomyocytes (Myo) (Ctl) and myocyte-derived progenitor cells (MDCs) demonstrated significant dedifferentiation of myocytes and identity of stemness, cell cycle progression and proliferation in MDCs after continuous culture in mitogen-rich medium for about 2 weeks. Total RNA was extracted from 3 batches of myocytes or MDCs; 100ug each was subjected to TLDA microRNA profiling after preamplification using ABI's kit. Cardiomyocyte (Myo, Ctl) was used as calibrator sample.

2010-09-22 | E-GEOD-24252 | 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