MicroRNA regulation and its effects on cellular transcriptome in Human Immnodeficiency Virus-1 (type-1) infected individuals with distinct viral load and CD4 cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Velpandi Ayyavoo
PROVIDER: E-GEOD-46018 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Human PBMCs were isolated from donors' blood. We used Taqman low density arrays to examine the differences in microRNA expression in the PBMCs of HIV seronegative individuals and individuals infected with low and high viral load.
2015-04-01 | GSE46018 | GEO
Project description:The goal of this study is to compare the base-line microRNA expression of asthmatic and healthy PBECs. PBECs were grown in-vitro up to passage 2 before harvest. RT-qPCR based microRNA array expression profiling. PBECs were isolated from 5 healthy and 5 asthmatic donors. Total cellular RNA from each sample was processed and analyzed independently.
2014-09-19 | E-GEOD-61563 | biostudies-arrayexpress
Project description:Reactive Oxygen Species (ROS) could be a stress factor that affects microRNA regulation and function in macrophages. The production of microRNAs (miRNA) is influenced by various stimuli, including environmental stresses. We hypothesized that ROS-associated stress could regulate macrophage miRNA synthesis. p47phox-/- mice have deficient NADPH oxidase activity resulting in decreased ROS production. We cultured bone marrow-derived macrophages (BMDM) from wild type (WT) and p47phox-/- mice and profiled miRNA expression using microarrays. The microarray data reveals that there are differences in the expression levels of different miRs, and our studies suggest functional crosstalk between ROS and miR-451 in the regulation of macrophage oxidant stress. Mouse bone marrow-derived macrophages (BMDMs) were obtained from WT (wild type) and p47phox-/- mice. MicroRNAs were isolated by using the mirVana miRNA kit, and a TaqMan rodent microRNA array (consisting of Megaplex RT Primers, Rodent Pool-A, Applied Biosystems) was used for microarray. The array enables quantitation of the expression levels of up to 380 microRNAs and controls. Rodent Pool A contains reverse transcription (RT) primers for 335 and 238 unique microRNAs for mouse and rat, respectively, plus 4 species-specific controls. The data were analyzed on RQ manager software (Qiagen, SA Biosciences) and normalized to the endogenous controls, and analyzed for fold change of miRs in WT compared to p47phox-/-.
2014-07-09 | E-GEOD-55189 | biostudies-arrayexpress
Project description:Human pancreatic islets were isolated from pancreas of deceased donors by Ricordi's procedure and cultured in CMRL 1066 medium additioned with human albumin. EVs were isolated from conditioned medium derived from islet culture after isolation. Once isolated, RNA of islets and islet-derived EVs was extracted and analyzed for microRNA expression within 48 hours after isolation.
2012-07-30 | E-MEXP-3691 | biostudies-arrayexpress
Project description:ANGPTL1-overexpressed CL1-5 cells were used to identify miRNAs which regulate EMT, cancer invasion and metastasis. We used microRNA Taqman Low Density Array to identify candidate miRNAs ANGPTL1-overexpressed CL1-5 cells were analyzed compare to vector control (pcDNA3.1) CL1-5 cells
2012-11-24 | E-GEOD-42481 | biostudies-arrayexpress
Project description:miRNAs have been proven to be very useful biomarkers, readily detectable in body fluids, particularly urine may be a valuable source to identify changes in miRNA levels that contribute to better differentiate prostate cancer (PCa) from benign prostate hyperplasia (BPH) cases. In order to characterize microRNA expression in urine samples from PCa, we analyzed expression of 376 microRNAs in 9 samples of PCa and 9 of BPH. The Normalized Ct values were compared between PCa and BPH. Statistical comparisons were made using Mann-Whitney U test, considering two different distributions. We found statiscally differences n expression for 21 miRNAs (Fold change >2 and P value<0.05). For the initial screening of all the studied samples, we selected only those with a concentration above 100 ng/ml, for a total of 9 samples of group of PCa and 9 BPH group. The isolated RNA was evaluated by measuring the absorbance at 260 nm and 280 nm. RNA aliquots from specimens were pooled and reverse transcription (RT) reaction was pweformed. In total, we formed 3 pools from BPH specimens and 3 from PCa ones. The RT product was used to perform a preamplification reaction. The product of preamplification teaction was loaded into the Taqman Homo sapiens microRNA Low density arrays (TLDA) panel A and amplification signal was detected using the 7900 FAST real time thermal cycler (ABI).
2012-07-12 | E-GEOD-39314 | biostudies-arrayexpress
Project description:Background: Many strategies to define subtypes and treat cancer relies on a presumption of either localized or widespread (poly)metastatic disease. We proposed an intermediate state of metastasis termed oligometastasis(es) characterized by limited metastatic progression and amenable to treatment by localized methods e.g. surgery or radiotherapy. Methods: To understand the biological basis of oligometastatic and polymetastatic progression, we analyzed microRNA expression patterns from lung tumor samples of patients with less than five metastases at first metastasis presentation and treated with metastasis-directed surgery. Results: Patients were stratified into four subgroups of oligo- and poly-metastatic progression based on the rate of metastatic progression over follow-up period. We prioritized microRNAs between the extremes of oligo- vs. poly-metastatic progression and validated their capacity to distinguish these phenotypes and predict survival in an independent validation dataset. Conclusions: Our results provide further evidence for the biological underpinnings of oligometastasis(es) and potential microRNA candidates to predict progression trajectories of patients and optimize corresponding metastasis-directed treatment. We collected tumor samples from 63 patients that (i) had between one and five metastasis(es) at first metastatic presentation and no clinical or radiologic evidence of metastases in the pleural, peritoneal, pericardial or retroperitoneal cavities,(ii) at the time of lung surgery, had every site of known metastases treated with definitive intent, and (iii) had a minimum of 16 months of follow-up after surgery was required. Total RNA were derived from FFPE metastatic tissue samples. Patient samples were subsequently classified into 3 groups: those from patients with high, intermediate and low rates of progression.
2012-06-13 | E-GEOD-38698 | biostudies-arrayexpress
Project description:Newborn Balb/c mice were injected with 1.5x10^6 fluorescent-forming units (ffu) of Rhesus rotavirus type-A or 0.9% NaCl (normal saline) intraperitoneally within 24 hours of birth to induce experimental model of biliary atresia. The extrahepatic bile ducts including gallbladder were microdissected en bloc at 3, 7 and 14 days after rhesus rotavirus or saline injection. TaqManM-BM-. Array Rodent MicroRNA Card v2.0 (A and B) were used to screen microRNAs whose expression was differently regulated after rhusus rotavirus injection compare to the normal saline controls. microRNA expression profiling. Each experimental conditon has 3 sets samples . Two to six extrahepatic bileducts were pooled prior to total RNA isolation depending on the size to ensure adequate RNA quantities to perform experiments quantifying microRNA expression.
2013-10-15 | E-GEOD-41593 | biostudies-arrayexpress
Project description:Endogenous molecules generated upon pathogen invasion or tissue damage serve as danger signals that activate host defence, however their precise immunological role remains unclear. Tenascin-C is an extracellular matrix glycoprotein that is specifically induced upon injury and infection. We have shown that its expression is required to generate an effective immune response to bacterial lipopolysaccharide (LPS) during experimental sepsis in vivo. Tenascin-C enables macrophage translation of pro-inflammatory cytokines upon LPS activation of toll-like receptor 4 (TLR4) and suppresses the synthesis of anti-inflammatory cytokines. It mediates post-transcriptional control of a specific subset of inflammatory mediators via induction of the microRNA miR-155. Thus tenascin-C plays a key role in regulating the inflammatory axis during pathogenic activation of TLR signaling. The data deposited here include the analysis of miRNA profile of tnc+/+ and tnc-/- bone marrow-derived macrophages (BMDMs) following stimulation with LPS for 8 hours. Bone marrow-derived macrophages (BMDMs) were cultured in complete DMEM medium, non-stimulated or stimulated for 8 hours with 100ng/ml LPS and total RNA was extracted. Samples were analysed with TaqMan Low Density Arrays (Applied Biosystems).
2012-10-18 | E-GEOD-41584 | biostudies-arrayexpress
Project description:To investigate the regulatory mechanisms governing the malignant signature of different gliomas we analyzed microRNA expression profiles in human tumor samples of world health organization (WHO) grade I (benign tumors), II (low grade tumors) and IV (high grade tumors) and from primary cultures obtained from tumor samples of grade II and IV. Patients This study included tumor samples histologically verified as astrocytic gliomas obtained from patients who had undergone craniotomy for microsurgical tumor removal. According to the revised WHO classification, tumors were diagnosed as: grade I or pilocytic astrocytomas; grade II or diffuse fibrillary astrocytomas; grade IV or glioblastoma multiforme. Primary cell cultures from grade II and grade IV gliomas were also obtained and miRNA expression in these cultures were analyzed RNA extraction Total RNA, including small RNA, was isolated from tissue samples using the mirVanaTM miRNA Isolation Kit (Ambion) following the standard protocol. The quantity and quality of the purified RNA was evaluated by spectrophotometric analysis and electrophoresis on denaturing gel of acrylamide. Multiplex Real-Time Quantitative Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR) The miRNAs were first converted to cDNA using Multiplex RT for TaqMan Array Human MicroRNA Panel. The RT Master mix included 100 mM each of dNTPs , 50 U/ml MultiScrabe reverse transcriptase (Applied Biosystems), 20 U/M-BM-5l RNase inhibitor (Applied Biosystems) and 10X RT Buffer. The 10 M-BM-5l reactions, including 7 M-BM-5l of RT master mix, 2 M-BM-5l of purified microRNA and 1 M-BM-5l of Multiplex RT Human primer pool (Applied Biosystem), were incubated in ice for 5 min and then in a thermal cycler for 30 min at 16M-BM-0C, 30 min at 42M-BM-0C, 5 min at 85M-BM-0C, and then hold at 4M-BM-0C. miRNA levels were normalized to the expression of small nucleolar RNAs, RNU44, RNU48 and RNU6B. All reverse transcriptase reactions, including no-template controls and RT controls, were run in duplicate. Real-time PCR was performed using a standard TaqMan PCR kit procedure on an M-bM-^@M-^\Real Time Fast 7900 HTM-bM-^@M-^] PCR System (Applied Biosystems). The 100 M-BM-5l PCR included 50 M-BM-5l RT product (before diluited 1:60) and 50 M-BM-5l TaqMan Universal PCR Master Mix (2X) (Applied Biosystems). The total volume were loaded into Card TaqMan Low Density Array Human MicroRNA Panel (Applied Biosystem) including a total of 384 human microRNAs publicated on databases www.sanger.ac.uk. The reaction cards was runned at 50M-BM-0C for 2 min and 95M-BM-0C for 10 min, followed by 40 cycles of 97M-BM-0C for 30s and 59,7M-BM-0C for 1 min. All reactions were run in triplicate. Analysis of data was performed using the SDS 2.3 software using the 2-M-bM-^HM-^FM-bM-^HM-^FCt (relative quantitative) method . The M-bM-^HM-^FCt of every miRNA was determined in relation to the endogenous control RNA U6 that was invariably expressed in all samples. The M-bM-^HM-^FM-bM-^HM-^FCt value was determined in relation to the calibrator, namely the normal brain tissue. Resulting data were grouped according to the tumor grading e selectioned using a cut-off value of 3. Results were expressed as M-bM-^@M-^\fold changeM-bM-^@M-^] over normal brain tissue. We analyzed two samples of grade I, two samples of grade II, two samples of grade IV gliomas. Four samples form norma brain were used as norma control. Primary cell cultures form grade II and grade IV samples were used for the analysis. All reverse transcriptase reactions, including no-template controls and RT controls, were run in triplicate.
2013-09-18 | E-GEOD-50924 | biostudies-arrayexpress