keyword
MENU ▼
Read by QxMD icon Read
search

muscle RNA-seq

keyword
https://www.readbyqxmd.com/read/28916639/small-rna-seq-during-acute-maximal-exercise-reveal-rnas-involved-in-vascular-inflammation-and-cardiometabolic-health
#1
Ravi Shah, Ashish S Yeri, Avash Das, Amanda Courtright-Lim, Olivia Ziegler, Ernest Gervino, Jeffrey Ocel, Pablo Quintero Pinzon, Luke Wooster, Cole Shields Bailey, Kahraman Tanriverdi, Lea Beaulieu, Jane E Freedman, Ionita Ghiran, Gregory D Lewis, Kendall Van Keuren-Jensen, Saumya Das
OBJECTIVE: Exercise improves cardiometabolic and vascular function, though mechanisms remain unclear. Our objective was to demonstrate the diversity of circulating extracellular RNA (ex-RNA) release during acute exercise in humans and its relevance to exercise-mediated benefits on vascular inflammation. Approach and Results: We performed plasma small RNA sequencing (RNA-seq) in 26 individuals undergoing symptom-limited maximal treadmill exercise, with replication of our top candidate miRNA in a separate cohort of 59 individuals undergoing bicycle ergometry...
September 15, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28915060/long-non-coding-rna-lnrpt-is-regulated-by-pdgf-bb-and-modulates-proliferation-of-pulmonary-artery-smooth-muscle-cells
#2
Jidong Chen, Jiao Guo, Xiaolei Cui, Yan Dai, Zhixiong Tang, Junle Qu, J Usha Raj, Qinghua Hu, Deming Gou
Pulmonary artery hypertension (PAH) is a rare and fatal disorder with extensive remodeling of pulmonary arteries mediated by hyperproliferation of pulmonary artery smooth muscle cell (PASMC). Aberrant platelet-derived growth factor (PDGF) activity can lead to hyperproliferation of PASMC, however, little is known about the role of long noncoding RNA (lncRNA) in this process. Using RNA sequencing (RNA-seq), we identified 725 lncRNAs in rat PASMC (RPASMC), 95 of which were expressed differentially in response to PDGF-BB treatment...
September 15, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28893664/single-cell-transcriptome-analysis-of-muscle-satellite-cells-reveals-widespread-transcriptional-heterogeneity
#3
Dong Seong Cho, Jason D Doles
Tissue specific stem cells are indispensable contributors to adult tissue maintenance, repair, and regeneration. In skeletal muscle, satellite cells (SCs) are the resident muscle stem cell population and are required to maintain skeletal muscle homeostasis throughout life. Increasing evidence suggests that SCs are a heterogeneous cell population with substantial biochemical and functional diversity. A major limitation in the field is an incomplete understanding of the nature and extent of this cellular heterogeneity...
September 8, 2017: Gene
https://www.readbyqxmd.com/read/28886574/comparative-transcriptome-analysis-of-fast-twitch-muscle-and-slow-twitch-muscle-in-takifugu-rubripes
#4
Kailun Gao, Zhicheng Wang, Xiaoxu Zhou, Haoze Wang, Derong Kong, Chen Jiang, Xiuli Wang, Zhiqiang Jiang, Xuemei Qiu
Fast twitch muscle and slow twitch muscle are two important organs of Takifugu rubripes. Both tissues are of ectodermic origin, and the differences between the two muscle fibers reflect the differences in their myofibril protein composition and molecular structure. In order to identify and characterize the gene expression profile in the two muscle fibers of T. rubripes, we generated 54 million and 44 million clean reads from the fast twitch muscle and slow twitch muscle, respectively, using RNA-Seq and identified a total of 580 fast-muscle-specific genes, 1533 slow-muscle-specific genes and 11,806 genes expressed by both muscles...
August 30, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28882000/integrative-deep-models-for-alternative-splicing
#5
Anupama Jha, Matthew R Gazzara, Yoseph Barash
Motivation: Advancements in sequencing technologies have highlighted the role of alternative splicing (AS) in increasing transcriptome complexity. This role of AS, combined with the relation of aberrant splicing to malignant states, motivated two streams of research, experimental and computational. The first involves a myriad of techniques such as RNA-Seq and CLIP-Seq to identify splicing regulators and their putative targets. The second involves probabilistic models, also known as splicing codes, which infer regulatory mechanisms and predict splicing outcome directly from genomic sequence...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28863190/transcriptome-analysis-of-the-pectoral-muscles-of-local-chickens-and-commercial-broilers-using-ribo-zero-ribonucleic-acid-sequencing
#6
Yanhua Zhang, Donghua Li, Ruili Han, Yanbin Wang, Guoxi Li, Xiaojun Liu, Yadong Tian, Xiangtao Kang, Zhuanjian Li
BACKGROUND: The molecular mechanisms underlying meat quality and muscle growth are not clear. The meat quality and growth rates of local chickens and commercial broilers are very different. The Ribo-Zero RNA-Seq technology is an effective means of analyzing transcript groups to clarify molecular mechanisms. The aim of this study was to provide a reference for studies of the differences in the meat quality and growth of different breeds of chickens. RESULTS: Ribo-Zero RNA-Seq technology was used to analyze the pectoral muscle transcriptomes of Gushi chickens and AA broilers...
2017: PloS One
https://www.readbyqxmd.com/read/28831113/rna-seq-reveals-microrna-expression-signature-and-genetic-polymorphism-associated-with-growth-and-muscle-quality-traits-in-rainbow-trout
#7
Bam Dev Paneru, Rafet Al-Tobasei, Brett Kenney, Timothy D Leeds, Mohamed Salem
The role of microRNA expression and genetic variation in microRNA-binding sites of target genes on growth and muscle quality traits is poorly characterized. We used RNA-Seq approach to investigate their importance on 5 growth and muscle quality traits: whole body weight (WBW), muscle yield, muscle crude-fat content, muscle shear force and whiteness. Phenotypic data were collected from 471 fish, representing 98 families (~5 fish/family) from a growth-selected line. Muscle microRNAs and mRNAs were sequenced from 22 families showing divergent phenotypes...
August 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28826478/extensive-alternative-splicing-transitions-during-postnatal-skeletal-muscle-development-are-required-for-calcium-handling-functions
#8
Amy E Brinegar, Zheng Xia, James Anthony Loehr, Wei Li, George Gerald Rodney, Thomas A Cooper
Postnatal development of skeletal muscle is a highly dynamic period of tissue remodeling. Here, we used RNA-seq to identify transcriptome changes from late embryonic to adult mouse muscle and demonstrate that alternative splicing developmental transitions impact muscle physiology. The first 2 weeks after birth are particularly dynamic for differential gene expression and alternative splicing transitions, and calcium-handling functions are significantly enriched among genes that undergo alternative splicing...
August 11, 2017: ELife
https://www.readbyqxmd.com/read/28821716/transcriptome-analysis-reveals-long-intergenic-non-coding-rnas-involved-in-skeletal-muscle-growth-and-development-in-pig
#9
Cheng Zou, Jingxuan Li, Wenzhe Luo, Long Li, An Hu, Yuhua Fu, Ye Hou, Changchun Li
Long intergenic non-coding RNAs (lincRNAs) play essential roles in numerous biological processes and are widely studied. The skeletal muscle is an important tissue that plays an essential role in individual movement ability. However, lincRNAs in pig skeletal muscles are largely undiscovered and their biological functions remain elusive. In this study, we assembled transcriptomes using RNA-seq data published in previous studies of our laboratory group and identified 323 lincRNAs in porcine leg muscle. We found that these lincRNAs have shorter transcript length, fewer exons and lower expression level than protein-coding genes...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28806168/mapping-the-mouse-allelome-reveals-tissue-specific-regulation-of-allelic-expression
#10
Daniel Andergassen, Christoph P Dotter, Daniel Wenzel, Verena Sigl, Philipp C Bammer, Markus Muckenhuber, Daniela Mayer, Tomasz M Kulinski, Hans-Christian Theussl, Josef M Penninger, Christoph Bock, Denise P Barlow, Florian M Pauler, Quanah J Hudson
To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles...
August 14, 2017: ELife
https://www.readbyqxmd.com/read/28800433/global-gene-expression-analysis-of-the-muscle-tissues-of-medaka-acclimated-to-low-and-high-environmental-temperatures
#11
Daisuke Ikeda, Hiroki Koyama, Nanami Mizusawa, Nobuhiro Kan-No, Engkong Tan, Shuichi Asakawa, Shugo Watabe
Medaka (Oryzias latipes) is a temperate eurythermal fish that is able to survive over a wide range of water temperatures ranging from near zero to over 30°C throughout the year; it maintains its normal physiological and biochemical processes through temperature acclimation. To determine the mechanisms involved in temperature acclimation of fish, the fast skeletal muscle tissues of medaka underwent global gene expression analysis using next-generation sequencing. Ten individuals were placed into two aquariums at 24°C...
August 2, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28795417/molecular-pathogenesis-of-human-prostate-basal-cell-hyperplasia
#12
Gervaise Henry, Alicia Malewska, Ryan Mauck, Jeffrey Gahan, Ryan Hutchinson, Jose Torrealba, Franto Francis, Claus Roehrborn, Douglas Strand
BACKGROUND: Understanding the molecular pathogenesis of distinct phenotypes in human benign prostatic hyperplasia (BPH) is essential to improving therapeutic intervention. Current therapies target smooth muscle and luminal epithelia for relief of lower urinary tract symptoms (LUTS) due to BPH, but basal cell hyperplasia (BCH) remains untargeted. The incidence of has been reported at 8-10%, but a molecular and cellular characterization has not been performed on this phenotype. METHODS: Using freshly digested tissue from surgical specimens, we performed RNA-seq analysis of flow cytometry-purified basal epithelia from 3 patients with and 4 patients without a majority BCH phenotype...
May 2017: Prostate
https://www.readbyqxmd.com/read/28755625/x-ray-irradiation-has-positive-effects-for-the-recovery-of-peripheral-nerve-injury-maybe-through-the-vascular-smooth-muscle-contraction-signaling-pathway
#13
Bo Jiang, Yong Zhang, Chang She, Jiaju Zhao, Kailong Zhou, Zhicheng Zuo, Xiaozhong Zhou, Peiji Wang, Qirong Dong
INTRODUCTION: It is well known that moderate to high doses of ionizing radiation have a toxic effect on the organism. However, there are few experimental studies on the mechanisms of LDR ionizing radiation on nerve regeneration after peripheral nerve injury. METHODS: We established the rats' peripheral nerve injury model via repaired Peripheral nerve injury nerve, vascular endothelial growth factor a and Growth associated protein-43 were detected from different treatment groups...
July 22, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28746361/identification-of-transcriptional-biomarkers-by-rna-sequencing-for-improved-detection-of-%C3%AE-2-agonists-abuse-in-goat-skeletal-muscle
#14
Luyao Zhao, Shuming Yang, Yongyou Cheng, Can Hou, Xinyong You, Jie Zhao, Ying Zhang, Wenjing He
In this paper, high-throughput RNA-sequencing (RNA-seq) was used to search for transcriptional biomarkers for β2-agonists. In combination with drug mechanisms, a smaller group of genes with higher detection accuracy was screened out. Unknown samples were first predicted by this group of genes, and liquid chromatograph tandem mass spectrometer (LC-MS/MS) was applied to positive samples to validate the biomarkers. The results of principal component analysis (PCA), hierarchical cluster analysis (HCA) and discriminant analysis (DA) indicated that the eight genes screened by high-throughput RNA-seq were able to distinguish samples in the experimental group and control group...
2017: PloS One
https://www.readbyqxmd.com/read/28742206/bioinformatics-analysis-of-rna-seq-data-revealed-critical-genes-in-colon-adenocarcinoma
#15
W-D Xi, Y-J Liu, X-B Sun, J Shan, L Yi, T-T Zhang
OBJECTIVE: RNA-seq data of colon adenocarcinoma (COAD) were analyzed with bioinformatics tools to discover critical genes in the disease. Relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated. MATERIALS AND METHODS: RNA-seq data of COAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. False positive discovery (FDR) < 0.05 and |log2 (fold change)|>1 were set as the cut-offs to screen out differentially expressed genes (DEGs)...
July 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28727021/physiology-and-endocrinology-symposium-the-effects-of-poor-maternal-nutrition-during-gestation-on-offspring-postnatal-growth-and-metabolism
#16
M L Hoffman, S A Reed, S M Pillai, A K Jones, K K McFadden, S A Zinn, K E Govoni
Poor maternal nutrition during gestation has been linked to poor growth and development, metabolic dysfunction, impaired health, and reduced productivity of offspring in many species. Poor maternal nutrition can be defined as an excess or restriction of overall nutrients or specific macro- or micronutrients in the diet of the mother during gestation. Interestingly, there are several reports that both restricted- and over-feeding during gestation negatively affect offspring postnatal growth with reduced muscle and bone deposition, increased adipose accumulation, and metabolic dysregulation through reduced leptin and insulin sensitivity...
May 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28717200/genome-wide-rna-sequencing-analysis-identifies-a-distinct-fibrosis-gene-signature-in-the-conjunctiva-after-glaucoma-surgery
#17
Cynthia Yu-Wai-Man, Nicholas Owen, Jonathan Lees, Aristides D Tagalakis, Stephen L Hart, Andrew R Webster, Christine A Orengo, Peng T Khaw
Fibrosis-related events play a part in most blinding diseases worldwide. However, little is known about the mechanisms driving this complex multifactorial disease. Here we have carried out the first genome-wide RNA-Sequencing study in human conjunctival fibrosis. We isolated 10 primary fibrotic and 7 non-fibrotic conjunctival fibroblast cell lines from patients with and without previous glaucoma surgery, respectively. The patients were matched for ethnicity and age. We identified 246 genes that were differentially expressed by over two-fold and p < 0...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28706492/lower-expression-of-slc27a1-enhances-intramuscular-fat-deposition-in-chicken-via-down-regulated-fatty-acid-oxidation-mediated-by-cpt1a
#18
Fengfang Qiu, Liang Xie, Jing-E Ma, Wen Luo, Li Zhang, Zhe Chao, Shaohao Chen, Qinghua Nie, Zhemin Lin, Xiquan Zhang
Intramuscular fat (IMF) is recognized as the predominant factor affecting meat quality due to its positive correlation with tenderness, juiciness, and flavor. Chicken IMF deposition depends on the balance among lipid synthesis, transport, uptake, and subsequent metabolism, involving a lot of genes and pathways, however, its precise molecular mechanisms remain poorly understood. In the present study, the breast muscle tissue of female Wenchang chickens (WC) (higher IMF content, 1.24 in D120 and 1.62 in D180) and female White Recessive Rock chickens (WRR; lower IMF content, 0...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28702480/dataset-on-transcriptional-profiles-and-the-developmental-characteristics-of-pdgfr%C3%AE-expressing-lung-fibroblasts
#19
Mehari Endale, Shawn Ahlfeld, Erik Bao, Xiaoting Chen, Jenna Green, Zach Bess, Matthew Weirauch, Yan Xu, Anne Karina Perl
The following data are derived from key stages of acinar lung development and define the developmental role of lung interstitial fibroblasts expressing platelet-derived growth factor alpha (PDGFRα). This dataset is related to the research article entitled "Temporal, spatial, and phenotypical changes of PDGFRα expressing fibroblasts during late lung development" (Endale et al., 2017) [1]. At E16.5 (canalicular), E18.5 (saccular), P7 (early alveolar) and P28 (late alveolar), PDGFRα(GFP) mice, in conjunction with immunohistochemical markers, were utilized to define the spatiotemporal relationship of PDGFRα(+) fibroblasts to endothelial, stromal and epithelial cells in both the proximal and distal acinar lung...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28688178/transcriptomic-analysis-identifies-a-role-of-pi3k-akt-signalling-in-the-responses-of-skeletal-muscle-to-acute-hypoxia-in-vivo
#20
Zhuohui Gan, Frank L Powell, Alexander C Zambon, Kyle S Buchholz, Zhenxing Fu, Karen Ocorr, Rolf Bodmer, Esteban A Moya, Jennifer C Stowe, Gabriel G Haddad, Andrew D McCulloch
KEY POINTS: Changes in gene expression that occur within hours of exposure to hypoxia in in vivo skeletal muscles remain unexplored. Two hours of hypoxia caused significant down-regulation of extracellular matrix genes followed by a shift at 6 h to altered expression of genes associated with the nuclear lumen while respiratory and blood gases were stabilized. Enrichment analysis of mRNAs classified by stability rates suggests an attenuation of post-transcriptional regulation within hours of hypoxic exposure, where PI3K-Akt signalling was suggested to have a nodal role by pathway analysis...
September 1, 2017: Journal of Physiology
keyword
keyword
118610
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"