Similar Datasets
Project description:qPCR profiling of mouse immune cell miRNAs
| PRJNA602706 | ENA
Project description:In the context of the Human Cell Atlas, the ImmGen consortium generated reference profiles by bulk RNAseq on finely sorted populations of immunocytes from human blood, healthy volunteers.
2023-03-20 | GSE227743 | GEO
Project description:We aimed at extending the repertoire of high-quality miRNA normalizers for reverse transcription-quantitative PCR (RT-qPCR) of human plasma with special emphasis on the extremely guanine-cytosine-rich portion of the miRNome. For high-throughput selection of stable candidates, microarray technology was preferred over small-RNA sequencing (sRNA-seq) since the latter underrepresented miRNAs with a guanine-cytosine (GC) content of at least 75% (p = 0.0002, n = 2). miRNA abundances measured on the microarray were ranked for consistency and uniformity using nine normalization approaches. The eleven most stable sequences included miRNAs of moderate, but also extreme GC content (45%–65%: miR-320d, miR-425-5p, miR-185-5p, miR-486-5p; 80%–95%: miR-1915-3p, miR-3656-5p, miR-3665-5p, miR-3960-5p, miR-4488-5p, miR-4497 and miR-4787-5p). In contrast, the seven extremely GC-rich miRNAs were not found in the two plasma miRNomes screened by sRNA-seq. Stem-loop RT-qPCR was employed for stability verification in 32 plasma samples of healthy male Caucasians (age range: 18–55 years). In general, inter-individual variance of miRNA abundance was low or very low as indicated by coefficient of variation (CV) values of 0.6%–8.2%. miR-3665 and miR-1915-3p outperformed in this analysis (CVs: 0.6 and 2.4%, respectively). The eight most stable sequences included four extremely GC-rich miRNAs (miR-1915-3p, miR-3665, miR-4787-5p and miR-4497). The best-performing duo normalization factor (NF) for the condition of human plasma, miR-320d and miR-4787-5p, also included a GC-extreme miRNA. In summary, the identification of extremely guanine-cytosine-rich plasma normalizers will help to increase accuracy of PCR-based miRNA quantification, thus raise the potential that miRNAs become markers for psychological stress reactions or early and precise diagnosis of clinical phenotypes. The novel miRNAs might also be useful for orthologous contexts considering their conservation in related animal genomes.
2022-07-25 | GSE209568 | GEO
Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs. In this study, Solexa deep sequencing technology was used for high-throughput analysis of miRNAs in a small RNA library isolated from four M. nipponense tissues (gill, hepatopancreas, muscle and hemocytes). In total, 9,227,356 reads were obtained, 4,293,155 of which were related to 267 unique miRNAs, including 203 conserved and 64 prawn-specific miRNAs. Furthermore, miRNA features including length distribution and end variations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways regulated by M. nipponense miRNAs. In addition, 880 co-expressed and 39 specific (25 normoxia-specific and 14 hypoxia-specific) miRNAs of four combined tissues of prawns that may be involved in the response to hypoxia were confirmed using miRNA microarray analysis. Real-time quantitative PCR (qPCR) analysis of eight miRNAs in the normoxia and hypoxia groups showed good concordance between the sequencing and qPCR data. This study provides the first large-scale identification and characterization of M. nipponense miRNAs and their potential targets, and represents a foundation for further characterization of their roles in the regulation of the diversity of hypoxia processes.
2016-06-01 | E-GEOD-72417 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs. In this study, Solexa deep sequencing technology was used for high-throughput analysis of miRNAs in a small RNA library isolated from four M. nipponense tissues (gill, hepatopancreas, muscle and hemocytes). In total, 9,227,356 reads were obtained, 4,293,155 of which were related to 267 unique miRNAs, including 203 conserved and 64 prawn-specific miRNAs. Furthermore, miRNA features including length distribution and end variations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways regulated by M. nipponense miRNAs. In addition, 880 co-expressed and 39 specific (25 normoxia-specific and 14 hypoxia-specific) miRNAs of four combined tissues of prawns that may be involved in the response to hypoxia were confirmed using miRNA microarray analysis. Real-time quantitative PCR (qPCR) analysis of eight miRNAs in the normoxia and hypoxia groups showed good concordance between the sequencing and qPCR data. This study provides the first large-scale identification and characterization of M. nipponense miRNAs and their potential targets, and represents a foundation for further characterization of their roles in the regulation of the diversity of hypoxia processes.
2016-06-01 | E-GEOD-72416 | biostudies-arrayexpress
Project description:Interventions: experimental group:surgical resection + Transcatheter Arterial Infusion Chemotherapy via tumor vessel;control group:surgical resection
Primary outcome(s): miRNA
Study Design: Randomized parallel controlled trial
| 2674732 | ecrin-mdr-crc
Project description:nCounter miRNA Expression Assay data for all profiled miRQC samples prepared by the miRQC Consortium. In this study, we systematically compared 12 commercially available miRNA expression platforms by measuring an identical set of standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from miRNA family members with varying homology. We developed novel and robust quality metrics to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, accuracy, specificity, and concordance of differential expression. miRQC Consortium multi-platform comparision. *This represents the NanoString component only
2013-12-30 | E-GEOD-49600 | biostudies-arrayexpress
Project description:Leishmania amazonensis is a protozoan that primarily infects macrophages and causes cutaneous leishmaniasis in humans. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at posttranscriptional levels. Previous work demonstrated changes in miRNA profile of host cells favoring parasite survivel. Thus, here we demonstrate that human macrophages upregulate several miRNAs on the initial time points of infection, including the hsa-miR-372, hsa-miR-373, and hsa-miR-520d, which present the same seed. Further functional analysis demonstrated that inhibition of the miR-372 impaired Leishmania survival in THP-1 macrophages and the effect was further enhanced with combinatorial inhibition of the miR-372/373/520d family, pointing to a cooperative mechanism. Our study demonstrated miRNA-dependent modulation of polyamines production, establishing permissive conditions for intracellular parasite survival.Our findings suggest that the miR-372/373/520d family may represent a potential target for the development of new therapeutic strategies against cutaneous leishmaniasis.
2023-09-11 | GSE242513 | GEO
Project description:iOmics miRNA data via qPCR quantification
| EGAD00010001308 | EGA
Project description:RT-qPCR of metabolite and ICB exposed organoids
| PRJNA804125 | ENA