MiRNA expression of the isolated human platelet-derived microparticle
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ABSTRACT:
PROVIDER: PRJNA638279 | ENA |
REPOSITORIES: ENA
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Project description:To analysis of potential functional components in PMPs to miRNAs, we have employed miRNA microarray expression profiling as a discovery platform to identified the miRNA content of PMPs.Human cord blood from healthy donors was used to isolated platelets and platelet-derived microparticles (PMPs) were isolated from activated platelets. First, for platelet isolation and purification, human platelets were isolated from the supernatant of umbilical cord blood after Ficoll-Hypaque density gradient centrifugation and pelleted by centrifugation at 2,000 × g for 20 min at RT. Second, the platelets were resuspended in saline (pH=7.4) containing 1 mM calcium and 1 U per mL thrombin for 15 min at 37°C. The PMPs were released into the supernatant. Contaminating remnant platelets were removed by centrifugation at 2,000 × g for 20 min at 4°C and filtered through a 0.8 μm filter unit (Millipore, America). Then, the supernatants containing PMPs were centrifuged at 20,000 × g for 120 min at 4°C.182 miRNAs were detected in the isolated human PMPs from five independent donors, although individual differences in miRNA expression were also observed. Thereafter, these miRNAs were ranked by expression level, and those expressed above the median level from each unique subject were considered to be abundantly expressed miRNAs. The intersection of abundantly expressed miRNAs in PMPs from each donor yielded 48 commonly expressed miRNAs in PMPs. Among these 48 miRNAs, miR-4454 ranked number 1, and its level was consistent in all samples examined.
2020-09-07 | GSE152078 | GEO
Project description:The aim of this project was to elucidate the microRNA profile of platelets and of platelet-derived microparticles isolated from clinical platelet concentrates treated or not with pathogen reduction technologies.
2020-04-09 | GSE138735 | GEO
Project description:To identify the miRNA expressing profiles of Platelet microparticles（PMPs, we have employed the Agilent Human miRNA 8×60K (Design ID:046064) microarray. Platelet microparticles. The platelets were derived from citrated blood of healthy human donors under an Institutional Review Board-approved protocol. Platelets were isolated after centrifugation of blood (1200r for 30 min at 21℃), then the supernatant (platelet-rich plasma) was centrifuged at 2000r for 30 min at 21℃, and the pellet containing platelets was resuspended in RPMI-1640 medium (HyClone, Logan, UT). Platelets were counted (Clinical Laboratory, Shanghai First Maternity and Infant Hospital, Shanghai) and adjusted to a density of 150 × 106 cells/mL before supplement with 1.5% ACD(sigma ) and stimulated with thrombin (1.0 u/mL; Takeda Austria) for 1 h. PMPs were in the supernatant after centrifugation at 4000r for 10 min at 4℃,then the supernatants were centrifuged at 50,000 × g for 60 min at 4 °C. The pellets containing MPs were resuspended in RPMI-1640 medium and quantified by BCA method.
2016-01-14 | GSE76789 | GEO
Project description:To identify the miRNA expressing profiles of Platelet microparticlesï¼PMPs, we have employed the Agilent Human miRNA 8Ã60K (Design ID:046064) microarray. Platelet microparticles. The platelets were derived from citrated blood of healthy human donors under an Institutional Review Board-approved protocol. Platelets were isolated after centrifugation of blood (1200r for 30 min at 21â), then the supernatant (platelet-rich plasma) was centrifuged at 2000r for 30 min at 21â, and the pellet containing platelets was resuspended in RPMI-1640 medium (HyClone, Logan, UT). Platelets were counted (Clinical Laboratory, Shanghai First Maternity and Infant Hospital, Shanghai) and adjusted to a density of 150 à 106 cells/mL before supplement with 1.5% ACD(sigma ) and stimulated with thrombin (1.0 u/mL; Takeda Austria) for 1 h. PMPs were in the supernatant after centrifugation at 4000r for 10 min at 4â,then the supernatants were centrifuged at 50,000 à g for 60 min at 4 °C. The pellets containing MPs were resuspended in RPMI-1640 medium and quantified by BCA method. The gene expressions of three independent paired PMPs from platelets stimulated by thrombin or apoptosis.
2016-01-14 | E-GEOD-76789 | biostudies-arrayexpress
Project description:Purpose: To assess the platelet miRNA pattern which is regulated in a Dicer-dependent manner, we conducted a global screen of platelet miRNA expression of murine platelets from Dicerlox/lox and DicerPf4∆/Pf4∆ mice using Next-generation deep sequencing analysis. Methods: Platelets were isolated from 10- to 12-week-old Dicerlox/lox and DicerPf4Δ/Pf4Δ mice of male sex. Total RNA including miRNA was isolated from murine platelets using the QIAsymphony RNA Kit. The sequencing library was prepared using the QIAseq miRNA Library Kit with 10 to 20 ng input. The libraries were pooled in an equimolar fashion and sequenced on a NovaSeq6000 as paired-end reads with a sequencing depth of >12 Mio clusters (i.e. read-pairs) per sample. Results: we were able to detect a total of 427 miRNAs in these platelets, of which 81 were significantly regulated (> |0.5| logFC threshold) in a Dicer-dependent manner. The majority of miRNAs were significantly downregulated, but a smaller proportion of miRNAs was slightly, but significantly upregulated in platelets lacking Dicer. Conclusions: this study discloses differential expression patterns of further platelet miRNAs that potentially link multiple intercellular processes and pathways implicated in several stages of the pathogenesis of myocardial I/R injury
2023-03-03 | GSE184523 | GEO
Project description:Platelet miRNA expression in NSCLC patients
| PRJNA1023956 | ENA
Project description:Results: MiRNA expression profiling of 1281 human miRNAs revealed relevant expression of 221 miRNAs consistently expressed in all samples at all time points. Correlation of platelet miRNA ranks was highly significant with data from other studies. Global distribution of miRNA expression was relatively similar in all subjects. No miRNA exhibited a significant effect of time at level 0.05. This finding was supported by exploratory analysis of predicted time effects from the mixed effects models. Furthermore, no significant effect of ASA could be found. Concerning the functional implication of the 20 most abundantly expressed miRNAs, we found 6 functional themes: nuclear import, cell cycle, transmembrane receptor protein serine/threonine kinase signaling pathway, regulation of kinase activity, pathways in cancer, and leukocyte differentiation. Conclusion: Our study shows that the platelet miRNA profile is remarkably stable in healthy subjects and is not affected by single-dose ASA treatment. For this reason, single-point analysis of platelet miRNA profile is reasonable when inter-individual differences are studied. The functional annotation network points toward additional extra-platelet effects of platelet miRNAs. We assessed the platelet miRNA profile blood in 5 volunteers at five time points over a time course of 10 days; 24 h prior to the last blood sampling, all subjects took 500 mg acetylsalicylic acid (ASA) once. Platelet miRNA was isolated from platelet-rich plasma which was leucocyte-depleted by negative bead separation. Then miRNA array analysis was performed on the isolated platelet miRNA. Temporal patterns and the effect of ASA were explored by a linear mixed effects model for each miRNA. For the 20 most abundantly expressed platelet miRNAs, a target gene search was performed by using miRWalk for validated and predicted targets. To visualize which molecular functions arerelated to those miRNAs, an annotation network was created by ClueGO, a Cytoscape plug-in.
2012-06-19 | E-GEOD-33215 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) regulate cell physiology by altering protein expression, but the biology of platelet miRNAs is largely unexplored. We tested whether platelet miRNA levels were associated with platelet reactivity by genome-wide profiling using platelet RNA from 19 healthy subjects. We found that human platelets express 284 miRNAs. Unsupervised hierarchical clustering of miRNA profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes. Seventy-four miRNAs were differentially expressed (DE) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response. Using whole genome mRNA expression data on these same subjects, we computationally generated a high-priority list of miRNA-mRNA pairs in which the DE platelet miRNAs had binding sites in 3'UTRs of DE mRNAs, and the levels were negatively correlated. Three miRNA-mRNA pairs (miR-200b:PRKAR2B, miR-495:KLHL5 and miR-107:CLOCK) were selected from this list and all 3 miRNAs knocked down protein expression from the target mRNA. Reduced activation from platelets lacking PRKAR2B supported these findings. In summary, (1) platelet miRNAs are able to repress expression of platelet proteins, (2) miRNA profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional miRNAs in platelets. Total RNA from the platelets of 19 donors was harvested and labeled with Hy3. Reference RNA (a pool of all samples) was labeled with Hy5. This submission represents the miRNA expression component of the study.
2011-09-26 | E-GEOD-27917 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) regulate cell physiology by altering protein expression, but the biology of platelet miRNAs is largely unexplored. We tested whether platelet miRNA levels were associated with platelet reactivity by genome-wide profiling using platelet RNA from 19 healthy subjects. We found that human platelets express 284 miRNAs. Unsupervised hierarchical clustering of miRNA profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes. Seventy-four miRNAs were differentially expressed (DE) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response. Using whole genome mRNA expression data on these same subjects, we computationally generated a high-priority list of miRNA-mRNA pairs in which the DE platelet miRNAs had binding sites in 3'UTRs of DE mRNAs, and the levels were negatively correlated. Three miRNA-mRNA pairs (miR-200b:PRKAR2B, miR-495:KLHL5 and miR-107:CLOCK) were selected from this list and all 3 miRNAs knocked down protein expression from the target mRNA. Reduced activation from platelets lacking PRKAR2B supported these findings. In summary, (1) platelet miRNAs are able to repress expression of platelet proteins, (2) miRNA profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional miRNAs in platelets.
2011-09-27 | GSE27917 | GEO
Project description:Platelet-derived exosomes (PL-Exos) have been widely used in tissue regeneration and inflammation regulation.Mass spectrometry-based proteomic analysis was used to study the protein content of platelet-derived exosomes and platelet lysates(PL).
2023-09-08 | PXD045219 |