Genome-wide maps of circulating miRNA biomarkers for Ulcerative Colitis
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Radha Duttagupta
PROVIDER: E-GEOD-32273 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Circulating miRNAs are an emerging class of biomarkers correlating their specific expression patterns to disease states. A considerable proportion of hematopoietically-derived miRNAs are present in plasma with the ability to confound the signature of true circulating miRNA species. We use microarray analysis to catalogue a list of 313 haemotopoetic miRNAs and analyze expression profiles of cell-free miRNAs in individual plasma fractions after calibrating for cellular miRNA signals. Comprehensive global maps of bona fide circulating miRNA species are presented, and inter-individual variability and gender-specific expression is explored in populations of healthy individuals. Healthy Caucasian individuals were used to segregate blood into 8 subfractions: white blood cells (WBC)/buffy coat, leukocytes, red blood cells (red blood cells (RBC)), cloudy supernatant (CS), supernatant 1 (S1), supernatant 2 (S2), pellet 1 (P1) and pellet 2 (P2) through differential centrifugation to understand the proportion of cellular miRNAs in each category.
2011-06-17 | E-GEOD-27230 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE27230: Analysis of the impact of cellular miRNA signatures on the profiles of circulating miRNA biomarkers (fractionation data) GSE27253: Analysis of the impact of cellular miRNA signatures on the profiles of circulating miRNA biomarkers (variability data) Refer to individual Series
2011-06-17 | E-GEOD-27256 | biostudies-arrayexpress
Project description:Circulating miRNAs are an emerging class of biomarkers correlating their specific expression patterns to disease states. A considerable proportion of hematopoietically-derived miRNAs are present in plasma with the ability to confound the signature of true circulating miRNA species. We use microarray analysis to catalogue a list of 313 haemotopoetic miRNAs and analyze expression profiles of cell-free miRNAs in individual plasma fractions after calibraiting for cellular miRNA signals. Comprehensive global maps of bona fide circulating miRNA species are presented, and inter-individual varibility and gender-specific expession is explored in populations of healthy individuals. Supernatant 1 (S1) fractions from 8 male and 10 female individuals.
2011-06-17 | E-GEOD-27253 | biostudies-arrayexpress
Project description:The aim of this experiment was to analyse the level of microRNAs circulating in plasma from two DLBCL patients during their treatment and one healthy donor with no history of cancer. The two DLBCL patients were selected based on their highly different response to first line chemotherapy (R-CHOP). One of them obtained a complete remission after first line, while the other presented a refractory disease.
2018-06-20 | E-MTAB-6063 | biostudies-arrayexpress
Project description:Microarray studies were performed to identify expression patterns by cryopreserved adipose stromal vascular fraction (SVF) preparations that were prepared by three different veterinary stem cell companies from the same source of canine adipose tissue. [Samples 1 - 3] Three equal samples of approximately 20 grams of adipose tissue were shipped on ice to 3 different companies which specialize in adipose-derived veterinary stem cell therapy. All 3 SVF preparations were cryopreserved at their respective facilities. Approximately one month later, cryopreserved samples were retrieved from all companies and transported frozen to the University of Kentucky for gene profiling and viability analysis. [Samples 4 - 11] Groups of cells (samples 5, 7, 9, 11) were treated by the stem cell company with photo-activated platelet-rich plasma (PRP) according to their proprietary procedures in order to enhance regenerative properties of the adipose stem cells. These PRP-treated cells were incubated in the investigator's lab for 6 hours at 37 degrees Celsius to allow for expression of genes that were induced by PRP treatment.
2014-03-05 | E-GEOD-55351 | biostudies-arrayexpress
Project description:We report RNA-sequencing data of 283 blood platelet samples, including 228 tumor-educated platelet (TEP) samples collected from patients with six different malignant tumors (non-small cell lung cancer, colorectal cancer, pancreatic cancer, glioblastoma, breast cancer and hepatobiliary carcinomas). In addition, we report RNA-sequencing data of blood platelets isolated from 55 healthy individuals. This dataset highlights the ability of TEP RNA-based 'liquid biopsies' in patients with several types with cancer, including the ability for pan-cancer, multiclass cancer and companion diagnostics. Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing EDTA anti-coagulant by standard centrifugation. Total RNA was extracted from the platelet pellet, subjected to cDNA synthesis and SMARTer amplification, fragmented by Covaris shearing, and prepared for sequencing using the Truseq Nano DNA Sample Preparation Kit. Subsequently, pooled sample libraries were sequenced on the Illumina Hiseq 2500 platform. All steps were quality-controlled using Bioanalyzer 2100 with RNA 6000 Picochip, DNA 7500 and DNA High Sensitivity chips measurements. For further downstream analyses, reads were quality-controlled using Trimmomatic, mapped to the human reference genome using STAR, and intron-spanning reads were summarized using HTseq. The processed data includes 285 samples (columns) and 57736 ensemble gene ids (rows). The supplementary data file (TEP_data_matrix.txt) contains the intron-spanning read counts, after data summarization by HTseq.
2015-10-30 | E-GEOD-68086 | biostudies-arrayexpress
Project description:Low-grade chronic inflammation plays an important role in the development of obesity and obesity-associated disorders such as insulin resistance, type 2 diabetes, the metabolic syndrome and atherosclerosis. One possible link between obesity and inflammation is the enhanced activation of circulating monocytes making them more prone to infiltration into the adipose and vascular tissues of obese persons. microRNAs are a class of small endogenous non-coding RNAs, which function as important regulators of inflammation by modulating gene expression. Therefore, microRNA analysis of circulating monocytes from control and obese patients will potentially provide insights into the pathophysiology of obesity and associated disorders and supply biomarkers for diagnostic purpose. The cohort comprised 6 lean age-matched controls (BMI: 20±0.8 kg/m2, mean±SEM) and 9 obese individuals without clinical symptoms of cardiovascular disease (BMI: 46±1.5 kg/m2, P<0.001 compared with lean controls). CD14+ monocytes were collected, total RNA was extracted and subjected to microRNA expression analysis. Samples consisted of CD14+ monocytes from 6 lean controls and 9 morbidly obese patients.
2012-05-17 | E-GEOD-34223 | biostudies-arrayexpress
Project description:Coronary artery disease (CAD) is the leading cause of human morbidity and mortality worldwide, underscoring the need to improve diagnostic strategies. Platelets play a major role, not only in the process of acute thrombosis during plaque rupture, but also in the formation of atherosclerosis itself. MicroRNAs are endogenous small non-coding RNAs that control gene expression and are expressed in a tissue and disease-specific manner. Therefore they have been proposed to be useful biomarkers. The aim of this study was to investigate whether differences in miRNA expression levels in platelets can be found (i) between patients with premature CAD and healthy controls and (ii) within healthy controls after and before aspirin and statin administration. In this case-control study we measured expression levels of platelet miRNAs using microarrays from 40 male patients with premature CAD and 40 age- and sex-matched healthy controls. Premature CAD was defined as a cardiac event before the age of 51 years. The patients were selected from the outpatient clinic of the Academic Medical Center (AMC) of Amsterdam, which is specialised in premature CAD. The control cohort was composed of 40 healthy Caucasian male volunteers, who were recruited by advertisement and who were matched with the cases for age and smoking habits. Individuals of this control cohort did not have a history of CVD, nor did they have a positive family history of CVD and they were not allowed to use any medication. Patients and controls were excluded when they suffered from diabetes. Most CAD patients use aspirin and statins as secondary prevention. The influence of these drugs on miRNA profiles is unknown. To assess the possible influence of medication on miRNA expression and to control for medication as confounding factor, we asked 27 volunteers in our control cohort to also use these drugs. We administered simvastatin 40 mg, once daily, for 6 weeks and during the last two weeks we added 100mg of acetyl salicylic acid, once daily. Blood samples including isolated platelets were collected at baseline in the absence of aspirin and statins and after six weeks of medication use. We also assessed platelet function using the Multiplate® Analyzer (Roche) in the absence of aspirin and statin use. In short, 300 µl whole blood was diluted with 300 µl 0.9% saline and stirred for 3 minutes at 37 ºC. Adenosine diphosphate (ADP) was added in a final concentration of 2.5 ?mol/L to initiate platelet aggregation. Aggregation was measured for 6 minutes and was reported in arbitrary aggregation units plotted against time. Also, the area under the aggregation curve (AUC) was measured. All samples were measured in the absence and presence of 200 ?mol/L indomethacin (20 min incubation with blood) to mimic the effect of aspirin use. We calculated the percentage reduction in AUC after incubation with indomethacin as an in vitro measure of the effect of aspirin use on whole blood platelet aggregation.
2015-06-22 | E-GEOD-59421 | biostudies-arrayexpress
Project description:Systems biology is an approach to comprehensively study complex interactions within a biological system. Most published systems vaccinology studies have utilized whole blood or peripheral blood mononuclear cells (PBMC) to monitor the immune response after vaccination. Because human blood is comprised of multiple hematopoietic cell types, the potential for masking responses of under-represented cell populations is increased when analyzing whole blood or PBMC. To investigate the contribution of individual cell types to the immune response after vaccination, we established a rapid and efficient method to purify human T and B cells, natural killer (NK) cells, myeloid dendritic cells (mDC), monocytes, and neutrophils from fresh venous blood. Purified cells were fractionated and processed in a single day. RNA-Seq and quantitative shotgun proteomics were performed to determine expression profiles for each cell type prior to and after inactivated seasonal influenza vaccination. Our results show that transcriptomic and proteomic profiles generated from purified immune cells differ significantly from PBMC. Differential expression analysis for each immune cell type also shows unique transcriptomic and proteomic expression profiles as well as changing biological networks at early time points after vaccination. This cell type-specific information provides a more comprehensive approach to monitor vaccine responses.
2015-01-08 | PXD001657 | Pride
Project description:Blood was sampled from severe burns patients over time as well as healthy subjects. Genome-wide expression analyses were conducted using the Affymetrix U133 plus 2.0 GeneChip™. The Inflammation and the Host Response to Injury Large-Scale Collaborative Research Program Blood was sampled from 244 severe burns patients over time as well as 35 healthy subjects who consented to blood sampling. Study subjects were treated under standard operating procedures to minimize treatment variations. Patients had burns covering >20% of the total body surface area and were admitted within 96 hours of injury. Genome-wide expression analyses were conducted using the Affymetrix U133 plus 2.0 GeneChip™.
2013-02-12 | E-GEOD-37069 | biostudies-arrayexpress