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

Disease-Associated SNPs From non-Coding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Lisha Zhu

PROVIDER: E-GEOD-66898 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Disease-Associated SNPs From non-Coding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells [ChIP-Seq]

Project description:We applied ChIP-Seq on two histone marks: H3K4me1 and H3K27ac in healthy human neutrophils. After peak calling, we obtained the peak regions enriched with H3K4me1 and H3K27ac histone marks and identifed aciive enhancers (H3K27ac+/H3K4me1+) and H3K27ac active enhancers (H3K27ac+/H3K4me1-) in human neutrophils and checked whether those enhancers are located in the LD blocks of 22 SNPs associtated with Juvenile Idiopathic Arthritis. Identification of active enhancers in human neutrohils

2015-06-12 | E-GEOD-66896 | biostudies-arrayexpress

Disease-Associated SNPs From non-Coding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells [RNA-Seq]

Project description:We sequenced mRNA from 3 neutrophil cells taken from 3 male adult to generate the gene expression profile of human neutrophil cells Examination of mRNA levels in human neutrophils.

2015-06-12 | E-GEOD-66895 | biostudies-arrayexpress

Gene Expression Profiles Distinguish Children with Inactive Polyarticular Juvenile Idiopathic Arthritis (JIA) with a Predilection to Flare

Project description:Gene expression profiles were obtained from 17 children with rheumatoid factor negative (RF-) polyarticular juvenile idiopathic arthritis (JIA). The disease was inactive in all patients at visit 1. Thee disease remained inactive at visit 2 for 9 patients, while the other 8 patients were experiencing a disease flare at visit 2. The goal of the study was to better understand the underlying molecular biology of flares in JIA Total RNA was obtained from PBMC at two different times in the course of disease 2 samples from each of 17 patients were collected and analyzed different times in the course of the disease

2013-12-14 | E-GEOD-26112 | biostudies-arrayexpress

Differentiating children with sepsis with and without acute respiratory distress syndrome using proteomics

Project description:Both sepsis and acute respiratory distress syndrome (ARDS) rely on imprecise clinical definitions leading to heterogeneity, which has contributed to negative trials. Because circulating protein/DNA complexes have been implicated in sepsis and ARDS, we aimed to develop a proteomic signature of DNA-bound proteins to discriminate between children with sepsis with and without ARDS. We performed a prospective case-control study in 12 children with sepsis with ARDS matched to 12 children with sepsis without ARDS on age, severity of illness score, and source of infection. We performed co-immunoprecipitation and downstream proteomics in plasma collected ≤ 24 h of intensive care unit admission. Expression profiles were generated, and a random forest classifier was used on differentially expressed proteins to develop a signature which discriminated ARDS. The classifier was tested in six independent blinded samples. Neutrophil and nucleosome proteins were over-represented in ARDS, including two S100A proteins, superoxide dismutase (SOD), and three histones. Random forest produced a 10-protein signature that accurately discriminated between children with sepsis with and without ARDS. This classifier perfectly assigned six independent blinded samples as having ARDS or not. We validated higher expression of the most informative discriminating protein, galectin-3-binding protein, in children with ARDS. Our methodology has applicability to isolation of DNA-bound proteins from plasma. Our results support the premise of a molecular definition of ARDS, and give preliminary insight into why some children with sepsis, but not others, develop ARDS.

2024-02-14 | PXD049377 | Pride

Characterization of the platelet transcriptome by RNA sequencing in patients with acute myocardial infarction.

Project description:Recent technological advances have made transcriptome sequencing (RNA-seq) possible in cells with low RNA copy number including platelets. Resulting studies have used RNA-seq in platelets isolated from healthy individuals to characterize the platelet transcriptome. However, platelets, possibly through gene expression changes, contribute to the etiology of and response to cardiovascular disease and events. To address this, we performed the largest human platelet RNA-seq analysis to date in 34 platelet samples: 16 ST-segment elevation myocardial infarction (STEMI), 16 non-STEMI (NSTEMI), and 2 controls. RNA-seq of platelet samples from 34 individuals: 16 with ST-elevation myocardial infarction (STEMI), 16 with non-STEMI, and 2 non-myocardial infarction controls

2015-09-15 | E-GEOD-65705 | biostudies-arrayexpress

Centenarians up-regulate the expression of microRNAs

Project description:microRNA analysis

2013-01-10 | E-MTAB-1231 | biostudies-arrayexpress

microRNA (miRNA) expression profiling of PBMCs of Parkinson's disease (PD) patients and controls

Project description:To investigate the role of miRNAs in the etiology of idiopathic PD, we conducted global miRNA expression profiling in peripheral blood mononuclear cells (PBMCs) of PD patients and controls. Total RNA was extracted from the PBMCs of 19 PD patients and 13 controls, labeled and hybridized to Exiqon microarrays spotted with probes for 733 human miRNAs.

2011-09-29 | E-GEOD-16658 | biostudies-arrayexpress

Expression analysis of stable chronic obstructive pulmonary disease and acute exacerbation of chronic obstructive pulmonary disease

Project description:Investigation of whole genome gene expression level changes of the dynamic gene profiling of peripheral blood mononuclear cells (PBMCs) from patients with AECOPD) on day1, 3 and 10, compared to the normal people and stable COPD patients. A five chip study using total RNA recovered from Peripheral Blood Mononuclear Cell of Peripheral Blood.Evaluating the dynamic gene profiling of peripheral blood mononuclear cells (PBMCs) from patients with AECOPD) on day1, 3 and 10 after the hospital admission, to compared with healthy controls or patients with stable COPD. Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.

2014-08-14 | E-GEOD-60399 | biostudies-arrayexpress

Blood biomarkers of pancreatic cancer associated diabetes identified by peripheral blood-based gene expression profiles

Project description:The prognosis of pancreatic cancer is still very poor, how to detect pancreatic cancer from high-risk group in an early stage is essential for improving its long-time survival. Therefore, the purpose of this study was to explore specific biomarkers that can differentiate pancreatic cancer-associated diabetes from type-2 diabetes for the early detection of pancreatic cancer. In the current study, we used global gene transcription analysis with affymetrix gene chip to identify genes specifically expressed in pancreatic cancer-associated diabetes mellitus from peripheral blood samples in stead of from tissue samples. 32 peripheral blood samples were collected for microarray experiments to find differentially expressed genes specific for pancreatic cancer associated diabetes, which included 8 patients diagnosed as pancreatic cancer with diabetes, 8 patients of pancreatic cancer without diabetes, 8 patients with diabetes mellitus>5years and 8 healthy controls. the comparision was done between pancreatic cancer with diabetes vs normal, pancreatic cancer vs normal and diabetes vs normal to identify a small group of genes that differently expressed in the pancreatic cancer with diabetes group.

2012-04-30 | E-GEOD-15932 | biostudies-arrayexpress

mRNA profiling by array of human Centenarians, normal aging and young people

Project description:We performed a transcriptomic analysis of mononuclear cells in blood in young people, septuagenarians, and centenarians.

2021-01-17 | E-MTAB-9988 | biostudies-arrayexpress