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miRNA next generation sequencing

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https://www.readbyqxmd.com/read/27908722/unexpected-regulation-of-mirna-abundance-during-adaptation-of-early-somite-mouse-embryos-to-diabetic-pregnancy
#1
J Zhao, T B M Hakvoort, A Jongejan, J M Ruijter, A H C van Kampen, W H Lamers
Maternal diabetes is one of major causes of congenital malformations in offspring, but the underlying mechanism is still unclear. MiRNAs play an important role in transcriptional and post-transcriptional regulation of gene expression. However, no miRNA expression profiling of hyperglycemic offspring are thus far available. Female mice were made diabetic with streptozotocin, treated with slow-release insulin tablets, and mated. MiRNA expression profiling with Next Generation Sequencing on the SOLiD5 platform was performed on 8 control and 5 hyperglycemic embryonic day (ED)8...
November 28, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27908684/identification-and-profiling-of-mirnas-in-overwintering-lissorhoptrus-oryzophilus-via-next-generation-sequencing
#2
Yang Shuang, Zhang Juhong, Wang Shang, Zhang Xinxin, Liu Yan, Xi Jinghui
MicroRNAs (miRNAs) are important regulators of various biological processes in organisms. Insects subjected to abiotic stress can regulate gene expression post-transcriptionally through the use of microRNAs. However, the role of miRNAs in response to cold stress in Lissorhoptrus oryzophilus Kuschel remains unknown. The rice water weevil, L. oryzophilus, is an invasive insect that is able to survive cold winters. To characterize changes in miRNAs in response to overwintering in L. oryzophilus, a comprehensive comparative analysis of microRNAs was performed involving an overwintering and a normal adult...
November 28, 2016: Cryobiology
https://www.readbyqxmd.com/read/27899663/large-scale-analysis-of-microrna-expression-epi-transcriptomic-features-and-biogenesis
#3
Dimitrios M Vitsios, Matthew P Davis, Stijn van Dongen, Anton J Enright
MicroRNAs are important genetic regulators in both animals and plants. They have a range of functions spanning development, differentiation, growth, metabolism and disease. The advent of next-generation sequencing technologies has made it a relatively straightforward task to detect these molecules and their relative expression via sequencing. There are a large number of published studies with deposited datasets. However, there are currently few resources that capitalize on these data to better understand the features, distribution and biogenesis of miRNAs...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895664/application-of-genomic-technologies-to-the-breeding-of-trees
#4
REVIEW
Maria L Badenes, Angel Fernández I Martí, Gabino Ríos, María J Rubio-Cabetas
The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27882772/mirnas-differentially-expressed-by-next-generation-sequencing-in-cord-blood-buffy-coat-samples-of-boys-and-girls
#5
Daneida Lizarraga, Karen Huen, Mary Combs, Maria Escudero-Fung, Brenda Eskenazi, Nina Holland
AIM: Differences in children's development and susceptibility to diseases and exposures have been observed by sex, yet human studies of sex differences in miRNAs are limited. MATERIALS & METHODS: The genome-wide miRNA expression was characterized by sequencing-based EdgeSeq assay in cord blood buffy coats from 89 newborns, and 564 miRNAs were further analyzed. RESULTS: Differential expression of most miRNAs was higher in boys. Neurodevelopment, RNA metabolism and metabolic ontology terms were enriched among miRNA targets...
November 24, 2016: Epigenomics
https://www.readbyqxmd.com/read/27872161/identification-of-urinary-exosomal-non-coding-rnas-as-novel-biomarkers-in-chronic-kidney-disease
#6
Rimpi Khurana, Glory Ranches, Simon Schafferer, Melanie Lukasser, Michael Rudnicki, Gert Mayer, Alexander Hüttenhofer
In chronic kidney disease (CKD), the decline in glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has extensively been studied, little is known about the role of urinary exosomes and their association with CKD. Exosomes are small, membrane-derived endocytic vesicles that contribute to cell-to-cell communication and are present in various body fluids, such as blood or urine...
November 21, 2016: RNA
https://www.readbyqxmd.com/read/27862381/mirna-and-pirna-expression-profiles-of-breeder-cock-testes-detected-by-next-generation-sequencing
#7
S R Wu, W Guo, Y L Li, X C Ren, X Y Lei, X Y Li, J H Yao, X J Yang
miRNAs are small non-coding regulatory RNAs that play key roles in diverse biological processes. In this study, we used the Solexa sequencing technique to profile miRNAs in breeder cock testes to illustrate their functions. A total of 663 co-expressed miRNAs and 3,180 co-expressed piRNAs were detected in three libraries. Based on Mir-X(™) miRNA qRT-PCR, three miRNAs representing low, medium and high expression levels according to the sequencing results were selected randomly to validate the miRNAs' expression profiles...
November 14, 2016: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/27845601/immediate-early-alcohol-responsive-mirna-expression-in-drosophila
#8
Alfredo Ghezzi, Marie Zomeno, Andrzej Z Pietrzykowski, Nigel S Atkinson
At the core of the changes characteristic of alcoholism are alterations in gene expression in the brain of the addicted individual. These changes are believed to underlie some of the neuroadaptations that promote compulsive drinking. Unfortunately, the mechanisms by which alcohol consumption produces changes in gene expression remain poorly understood. MicroRNAs (miRNAs) have emerged as important regulators of gene expression because they can coordinately modulate the translation efficiency of large sets of specific mRNAs...
November 15, 2016: Journal of Neurogenetics
https://www.readbyqxmd.com/read/27826915/mirna-isolation-from-plants-rich-in-polysaccharides-and-polyphenols
#9
K K Sabu, Fasiludeen Nadiya, Narayanannair Anjali
MicroRNAs (miRNAs) are a group of 18-22-nucleotide-long noncoding RNAs, which show wide array of roles in various biological and metabolic processes in both animals and plants. They are formed endogenously and have evolutionary conserved sequences. RNA quality is extremely important for sequencing miRNAs using next-generation sequencing platforms. However, isolation and quantification of miRNAs from plant samples are often technically difficult and recovery of miRNAs from total RNA might be problematic. Degradation of RNA weakens the true miRNAs present in the sample, hence it is crucial to use a protocol that effectively retains good integrity miRNAs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27825380/identification-and-characterization-of-micrornas-expressed-in-the-african-malaria-vector-anopheles-funestus-life-stages-using-high-throughput-sequencing
#10
Mushal Allam, Belinda L Spillings, Hiba Abdalla, Darlington Mapiye, Lizette L Koekemoer, Alan Christoffels
BACKGROUND: Over the past several years, thousands of microRNAs (miRNAs) have been identified in the genomes of various insects through cloning and sequencing or even by computational prediction. However, the number of miRNAs identified in anopheline species is low and little is known about their role. The mosquito Anopheles funestus is one of the dominant malaria vectors in Africa, which infects and kills millions of people every year. Therefore, small RNA molecules isolated from the four life stages (eggs, larvae, pupae and unfed adult females) of An...
November 8, 2016: Malaria Journal
https://www.readbyqxmd.com/read/27812362/high-throughput-sequencing-reveals-h2o2-stress-associated-micrornas-and-a-potential-regulatory-network-in-brachypodium-distachyon-seedlings
#11
Dong-Wen Lv, Shoumin Zhen, Geng-Rui Zhu, Yan-Wei Bian, Guan-Xing Chen, Cai-Xia Han, Zi-Tong Yu, Yue-Ming Yan
Oxidative stress in plants can be triggered by many environmental stress factors, such as drought and salinity. Brachypodium distachyon is a model organism for the study of biofuel plants and crops, such as wheat. Although recent studies have found many oxidative stress response-related proteins, the mechanism of microRNA (miRNA)-mediated oxidative stress response is still unclear. Using next generation high-throughput sequencing technology, the small RNAs were sequenced from the model plant B. distachyon 21 (Bd21) under H2O2 stress and normal growth conditions...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27791479/two-distinct-extracellular-rna-signatures-released-by-a-single-cell-type-identified-by-microarray-and-next-generation-sequencing
#12
Cecilia Lässer, Ganesh Vilas Shelke, Ashish Yeri, Dae-Kyum Kim, Rossella Crescitelli, Stefania Raimondo, Margareta Sjöstrand, Yong Song Gho, Kendall Van Keuren Jensen, Jan Lötvall
Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not...
October 28, 2016: RNA Biology
https://www.readbyqxmd.com/read/27787800/approaches-to-detect-microrna-expression-in-t-cell-subsets-and-t-cell-differentiation
#13
Silvia Monticelli, Tarmo Äijö, Sara Trifari
MicroRNAs (miRNAs) are crucial components of the molecular networks regulating differentiation and responses of T lymphocytes in health and disease. It is therefore essential to rely on robust methods of qualitative and quantitative investigation of miRNA expression in T cell subsets, and during T cell activation and differentiation. Here, we focus on different methods for miRNA analysis, including Northern blots, quantitative RT-PCR, and next-generation sequencing, and we discuss advantages and disadvantages of each method...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27780738/next-generation-sequencing-based-small-rna-profiling-of-cerebrospinal-fluid-exosomes
#14
Yohsuke Yagi, Takuya Ohkubo, Hideya Kawaji, Akira Machida, Haruka Miyata, Saori Goda, Sugata Roy, Yoshihide Hayashizaki, Harukazu Suzuki, Takanori Yokota
MicroRNAs (miRNAs), particularly those found in human body fluids, have been suggested as potential biomarkers. Among various body fluids, the cerebrospinal fluid (CSF) shows promise as a profiling target for diagnosis and monitoring of neurological diseases. However, relevant genome-scale studies are limited and no studies have profiled exosomal miRNAs in CSF. Therefore, we conducted a next-generation sequencing-based genome-wide survey of small RNAs in the exosomal and non-exosomal (supernatant) fractions of healthy human CSF as well as serum in each donor...
October 22, 2016: Neuroscience Letters
https://www.readbyqxmd.com/read/27724902/identification-and-differential-regulation-of-micrornas-in-response-to-methyl-jasmonate-treatment-in-lycoris-aurea-by-deep-sequencing
#15
Sheng Xu, Yumei Jiang, Ning Wang, Bing Xia, Yilong Jiang, Xiaodan Li, Zhengzhi Zhang, Yikui Li, Ren Wang
BACKGROUND: Lycoris aurea is a medicine-valuable and ornamental herb widely distributed in China. Former studied have showed that methyl jasmonate (MJ) treatment could increase the content of glanthamine-a worldwide medicine for symptomatic treatment of Alzheimer's disease in genus Lycoris plants. To explore the possible role of miRNAs in the regulation of jasmonic acid signaling pathway and uncover their potential correlations, we investigated the expression profiles of small RNAs (sRNAs) and their targets in Lycoris aurea, with MJ treatment by using next-generation deep sequencing...
October 10, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27722582/spire-a-modular-pipeline-for-eqtl-analysis-of-rna-seq-data-reveals-a-regulatory-hotspot-controlling-mirna-expression-in-c-elegans
#16
Ivan Kel, Zisong Chang, Nadia Galluccio, Margherita Romeo, Stefano Beretta, Luisa Diomede, Alessandra Mezzelani, Luciano Milanesi, Christoph Dieterich, Ivan Merelli
The interpretation of genome-wide association study is difficult, as it is hard to understand how polymorphisms can affect gene regulation, in particular for trans-regulatory elements located far from their controlling gene. Using RNA or protein expression data as phenotypes, it is possible to correlate their variations with specific genotypes. This technique is usually referred to as expression Quantitative Trait Loci (eQTLs) analysis and only few packages exist for the integration of genotype patterns and expression profiles...
September 22, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27701455/regulation-of-hbegf-by-micro-rna-for-survival-of-developing-human-trophoblast-cells
#17
Chandni V Jain, Philip Jessmon, Brian A Kilburn, Meritxell Jodar, Edward Sendler, Stephen A Krawetz, D Randall Armant
INTRODUCTION: The growth factor HBEGF is upregulated post-transcriptionally in the low O2 environment of the human placenta during the first 10 weeks of pregnancy. We have examined the possible roles of HBEGF turnover and micro-RNA (miRNA) in its regulation by O2 in human first trimester trophoblast. METHODS: HTR-8/SVneo trophoblast cells were cultured at 2% or 20% O2. The cells were transfected with a dual luciferase reporter construct (psiCHECK-2) containing no insert (control), the HBEGF 3' untranslated region (3'UTR), or sub-regions of the 3'UTR, as well as with siRNA for DGCR8...
2016: PloS One
https://www.readbyqxmd.com/read/27686613/comprehensive-analysis-of-microrna-signature-of-mouse-pancreatic-acini-overexpression-of-mir-21-3p-in-acute-pancreatitis
#18
Ajay Kumar Dixit, Anne E Sarver, Zuobiao Yuan, John George, Usman Barlass, Hassam Cheema, Archana Sareen, Sulagna Banerjee, Vikas Dudeja, Rajinder Dawra, Subbaya Subramanian, Ashok K Saluja
In the current study, we have characterized the global miRNA expression profile in mouse pancreatic acinar cells and during acute pancreatitis using next-generation RNA sequencing. We identified 324 known and six novel miRNAs that are expressed in mouse pancreatic acinar cells. In the basal state, miR-148a-3p, miR-375-3p, miR-217-5p, and miR-200a-3p were among the most abundantly expressed, whereas miR-24-5p and miR-421-3p were the least abundant. Treatment of acinar cells with caerulein (100 nM) and taurolithocholic acid 3-sulfate [TLC-S (250 μM)] induced numerous changes in miRNA expression profile...
November 1, 2016: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/27682205/impact-of-endurance-exercise-training-on-adipocyte-microrna-expression-in-overweight-men
#19
Thomas Tsiloulis, Joshua Pike, David Powell, Fernando J Rossello, Benedict J Canny, Ruth C R Meex, Matthew J Watt
Adipocytes are major regulators of metabolism and endurance exercise training improves adipocyte function; however, the molecular mechanisms that regulate chronic adaptive responses remain unresolved. microRNAs (miRNAs) influence adipocyte differentiation and metabolism. Accordingly, we aimed to determine whether adipocyte miRNA expression is responsive to exercise training and to identify exercise-responsive miRNAs that influence adipocyte metabolism. Next generation sequencing was used to profile miRNA expression of adipocytes that were isolated from subcutaneous abdominal (ABD) and gluteofemoral (GF) adipose tissue of overweight men before and after 6 wk of endurance exercise training...
September 28, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27666482/gene-expression-profiling-of-brain-samples-from-patients-with-lewy-body-dementia
#20
Maciej Pietrzak, Audrey Papp, Amanda Curtis, Samuel K Handelman, Maria Kataki, Douglas W Scharre, Grzegorz Rempala, Wolfgang Sadee
Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative disorder in the elderly. The development and progression of DLB remain unclear. In this study we used next generation sequencing to assess RNA expression profiles and cellular processes associated with DLB in the anterior cingulate cortex, a brain region affected by DLB pathology. The expression measurements were made in autopsy brain tissues from 8 DLB subjects and 10 age-matched controls using AmpliSeq technology with ion torrent sequencing...
October 28, 2016: Biochemical and Biophysical Research Communications
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