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muscle RNA-seq

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https://www.readbyqxmd.com/read/28058586/key-genes-in-stomach-adenocarcinoma-identified-via-network-analysis-of-rna-seq-data
#1
Li Shen, Lizhi Zhao, Jiquan Tang, Zhiwei Wang, Weisong Bai, Feng Zhang, Shouli Wang, Weihua Li
RNA-seq data of stomach adenocarcinoma (STAD) were analyzed to identify critical genes in STAD. Meanwhile, relevant small molecule drugs, transcription factors (TFs) and microRNAs (miRNAs) were also investigated. Gene expression data of STAD were downloaded from The Cancer Genome Atlas (TCGA). Differential analysis was performed with package edgeR. Relationships with correlation coefficient > 0.6 were retained in the gene co-expression network. Functional enrichment analysis was performed for the genes in the network with DAVID and KOBASS 2...
January 5, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28057818/dna-methylation-assessment-from-human-slow-and-fast-twitch-skeletal-muscle-fibers
#2
Gwenaelle Begue, Ulrika Raue, Bozena Jemiolo, Scott W Trappe
A new application of the Reduced Representation Bisulfite Sequencing method was developed using low-DNA input to investigate the epigenetic profile of human slow- and fast-twitch skeletal muscle fibers. Successful library construction was completed with as little as 15 ng of DNA and high quality sequencing data were obtained with 32 ng of DNA. Analysis identified 143,160 differentially methylated CpG-sites across 14,046 genes. In both fiber types, selected genes predominantly expressed in slow or fast fibers were hypomethylated, which was supported by the RNA-Seq analysis...
January 5, 2017: Journal of Applied Physiology
https://www.readbyqxmd.com/read/28045018/targeted-rna-seq-profiling-of-splicing-pattern-in-the-dmd-gene-exons-are-mostly-constitutively-spliced-in-human-skeletal-muscle
#3
Anne-Laure Bougé, Eva Murauer, Emmanuelle Beyne, Julie Miro, Jessica Varilh, Magali Taulan, Michel Koenig, Mireille Claustres, Sylvie Tuffery-Giraud
We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) NB transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28026080/transcriptomic-gene-profiling-of-porcine-muscle-tissue-depending-on-histological-properties
#4
Katarzyna Ropka-Molik, Anna Bereta, Kacper Żukowski, Katarzyna Piórkowska, Artur Gurgul, Grzegorz Żak
In pig, the histological profile of muscle tissue, especially the proportion of individual fiber types, is one of the main factors affecting meat quality properties. In the present research, RNA sequencing (RNA-seq) by using next generation sequencing method was applied to estimate the whole gene expression profile of Longissimus lumborum muscle of pigs (Large White breed) differing in the percentage of two fiber types (slow-twitch (type I) fibers and fast-twitch glycolytic (type IIB) fibers). The RNA-seq approach allowed us to identify 355 differentially expressed genes (DEGs) indicated as significant (false discovery rate-adjusted P < 0...
December 27, 2016: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/28011237/estradiol-regulates-expression-of-mirnas-associated-with-myogenesis-in-rainbow-trout
#5
Prasanthi P Koganti, Jian Wang, Beth Cleveland, Hao Ma, Gregory M Weber, Jianbo Yao
17β-Estradiol (E2) is a steroid hormone that negatively affects muscle growth in rainbow trout, but the mechanism associated with this response is not fully understood. To better characterize the effects of E2 on muscle, we identified differentially regulated microRNAs (miRNAs) and muscle atrophy-related transcripts in juvenile rainbow trout exposed to E2. Small RNA-Seq analysis of E2-treated vs. control muscle identified 36 differentially expressed miRNAs including those known to be involved in myogenesis, cell cycle, apoptosis, and cell death...
December 21, 2016: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28008606/derivation-of-marker-gene-signatures-from-human-skin-and-their-use-in-the-interpretation-trancriptional-changes-associated-with-dermatological-disorders
#6
Barbara Bo-Ju Shih, Ajit Johnson Nirmal, Denis John Headon, Arne Nalpon Akbar, Neil Andrew Mabbott, Tom Charles Freeman
Numerous studies have explored the altered transcriptional landscape associated with skin diseases to understand the nature of these disorders. However, data interpretation represents a significant challenge due to a lack of good maker sets for many of the specialised cell types that make up this tissue, whose composition may fundamentally alter during disease. Here we have sought to derive expression signatures that define the various cell types and structures that make up human skin, and demonstrate how they can be used to aid the interpretation of transcriptomic data derived from this organ...
December 23, 2016: Journal of Pathology
https://www.readbyqxmd.com/read/28005961/comparative-transcriptomic-study-of-muscle-provides-new-insights-into-the-growth-superiority-of-a-novel-grouper-hybrid
#7
Ying Sun, Yu Huang, Guojun Hu, Xinhui Zhang, Zhiqiang Ruan, Xiaomeng Zhao, Chuanyu Guo, Zhujing Tang, Xiaofeng Li, Xinxin You, Haoran Lin, Yong Zhang, Qiong Shi
Grouper (Epinephelus spp.) is a group of fish species with great economic importance in Asian countries. A novel hybrid grouper, generated by us and called the Hulong grouper (Hyb), has better growth performance than its parents, E. fuscoguttatus (Efu, ♀) and E. lanceolatus (Ela, ♂). We previously reported that the GH/IGF (growth hormone/insulin-like growth factor) system in the brain and liver contributed to the superior growth of the Hyb. In this study, using transcriptome sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR), we analyzed RNA expression levels of comprehensive genes in the muscle of the hybrid and its parents...
2016: PloS One
https://www.readbyqxmd.com/read/27996962/an-atlas-of-transcriptional-chromatin-accessibility-and-surface-marker-changes-in-human-mesoderm-development
#8
Pang Wei Koh, Rahul Sinha, Amira A Barkal, Rachel M Morganti, Angela Chen, Irving L Weissman, Lay Teng Ang, Anshul Kundaje, Kyle M Loh
Mesoderm is the developmental precursor to myriad human tissues including bone, heart, and skeletal muscle. Unravelling the molecular events through which these lineages become diversified from one another is integral to developmental biology and understanding changes in cellular fate. To this end, we developed an in vitro system to differentiate human pluripotent stem cells through primitive streak intermediates into paraxial mesoderm and its derivatives (somites, sclerotome, dermomyotome) and separately, into lateral mesoderm and its derivatives (cardiac mesoderm)...
December 20, 2016: Scientific Data
https://www.readbyqxmd.com/read/27939935/catalase-deletion-promotes-prediabetic-phenotype-in-mice
#9
Claire Heit, Stephanie Marshall, Surrendra Singh, Xiaoqing Yu, Georgia Charkoftaki, Hongyu Zhao, David J Orlicky, Kristofer S Fritz, David C Thompson, Vasilis Vasiliou
Hydrogen peroxide is produced endogenously and can be toxic to living organisms by inducing oxidative stress and cell damage. However, it has also been identified as a signal transduction molecule. By metabolizing hydrogen peroxide, catalase protects cells and tissues against oxidative damage and may also influence signal transduction mechanisms. Studies suggest that acatalasemic individuals (i.e., those with very low catalase activity) have a higher risk for the development of diabetes. We now report catalase knockout (Cat(-/-)) mice, when fed a normal (6...
December 8, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27936208/developmental-stage-muscle-and-genetic-type-modify-muscle-transcriptome-in-pigs-effects-on-gene-expression-and-regulatory-factors-involved-in-growth-and-metabolism
#10
Miriam Ayuso, Almudena Fernández, Yolanda Núñez, Rita Benítez, Beatriz Isabel, Ana I Fernández, Ana I Rey, Antonio González-Bulnes, Juan F Medrano, Ángela Cánovas, Clemente J López-Bote, Cristina Óvilo
Iberian pig production includes purebred (IB) and Duroc-crossbred (IBxDU) pigs, which show important differences in growth, fattening and tissue composition. This experiment was conducted to investigate the effects of genetic type and muscle (Longissimus dorsi (LD) vs Biceps femoris (BF)) on gene expression and transcriptional regulation at two developmental stages. Nine IB and 10 IBxDU piglets were slaughtered at birth, and seven IB and 10 IBxDU at four months of age (growing period). Carcass traits and LD intramuscular fat (IMF) content were measured...
2016: PloS One
https://www.readbyqxmd.com/read/27930992/alteration-of-development-and-gene-expression-induced-by-in-ovo-nanoinjection-of-3-hydroxybenzo-c-phenanthrene-into-japanese-medaka-oryzias-latipes-embryos
#11
Kun Chen, Yuki Tsutsumi, Shuhei Yoshitake, Xuchun Qiu, Hai Xu, Yasuyuki Hashiguchi, Masato Honda, Kosuke Tashiro, Kei Nakayama, Takeshi Hano, Nobuo Suzuki, Kazuichi Hayakawa, Yohei Shimasaki, Yuji Oshima
Benzo[c]phenanthrene (BcP) is a highly toxic polycyclic aromatic hydrocarbon (PAHs) found throughout the environment. In fish, it is metabolized to 3-hydroxybenzo[c]phenanthrene (3-OHBcP). In the present study, we observed the effects of 1nM 3-OHBcP on the development and gene expression of Japanese medaka (Oryzias latipes) embryos. Embryos were nanoinjected with the chemical after fertilization. Survival, developmental stage, and heart rate of the embryos were observed, and gene expression differences were quantified by messenger RNA sequencing (mRNA-Seq)...
January 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/27917881/distinct-and-shared-determinants-of-cardiomyocyte-contractility-in-multi-lineage-competent-ethnically-diverse-human-ipscs
#12
Martin L Tomov, Zachary T Olmsted, Haluk Dogan, Eda Gongorurler, Maria Tsompana, Hasan H Otu, Michael Buck, Eun-Ah Chang, Jose Cibelli, Janet L Paluh
The realization of personalized medicine through human induced pluripotent stem cell (iPSC) technology can be advanced by transcriptomics, epigenomics, and bioinformatics that inform on genetic pathways directing tissue development and function. When possible, population diversity should be included in new studies as resources become available. Previously we derived replicate iPSC lines of African American, Hispanic-Latino and Asian self-designated ethnically diverse (ED) origins with normal karyotype, verified teratoma formation, pluripotency biomarkers, and tri-lineage in vitro commitment...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27914205/mitochondrial-genotype-and-phenotypic-plasticity-of-gene-expression-in-response-to-cold-acclimation-in-killifish
#13
Timothy M Healy, Heather J Bryant, Patricia M Schulte
Adjustments of aerobic metabolic processes are critical components of organismal responses to environmental change that require tight co-ordination between the nuclear and mitochondrial genomes. Intraspecific differences in mitochondrial genotype can affect gene transcription in both genomes. Thus, variation in mitochondrial genotype may be associated with differences in the plasticity of gene expression when organisms are faced with changes in environmental conditions. Cold acclimation is known to result in metabolic responses involving increases in mitochondrial amount and capacity, suggesting that low temperatures may pose a particular challenge when co-ordinating the functions of the nuclear and mitochondrial genomes...
December 3, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27884102/gene-expression-profile-of-intramuscular-muscle-in-nellore-cattle-with-extreme-values-of-fatty-acid
#14
Mariana P Berton, Larissa F S Fonseca, Daniela F J Gimenez, Bruno L Utembergue, Aline S M Cesar, Luiz L Coutinho, Marcos Vinicius A de Lemos, Carolyn Aboujaoude, Angélica S C Pereira, Rafael M de O Silva, Nedenia B Stafuzza, Fabieli L B Feitosa, Hermenegildo L J Chiaia, Bianca F Olivieri, Elisa Peripolli, Rafael L Tonussi, Daniel M Gordo, Rafael Espigolan, Adrielle M Ferrinho, Lenise F Mueller, Lucia G de Albuquerque, Henrique N de Oliveira, Susan Duckett, Fernando Baldi
BACKGROUND: Fatty acid type in beef can be detrimental to human health and has received considerable attention in recent years. The aim of this study was to identify differentially expressed genes in longissimus thoracis muscle of 48 Nellore young bulls with extreme phenotypes for fatty acid composition of intramuscular fat by RNA-seq technique. RESULTS: Differential expression analyses between animals with extreme phenotype for fatty acid composition showed a total of 13 differentially expressed genes for myristic (C14:0), 35 for palmitic (C16:0), 187 for stearic (C18:0), 371 for oleic (C18:1, cis-9), 24 for conjugated linoleic (C18:2 cis-9, trans11, CLA), 89 for linoleic (C18:2 cis-9,12 n6), and 110 genes for α-linolenic (C18:3 n3) fatty acids...
November 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27875983/liver-transcriptome-response-to-hyperthermic-stress-in-three-distinct-chicken-lines
#15
Xi Lan, John C F Hsieh, Carl J Schmidt, Qing Zhu, Susan J Lamont
BACKGROUND: High ambient temperatures cause stress in poultry, especially for broiler lines, which are genetically selected for rapid muscle growth. RNA-seq technology provides powerful insights into environmental response from a highly metabolic tissue, the liver. We investigated the effects of acute (3 h, 35 °C) and chronic (7d of 35 °C for 7 h/d) heat stress on the liver transcriptome of 3-week-old chicks of a heat-susceptible broiler line, a heat-resistant Fayoumi line, and their advanced intercross line (AIL)...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27864233/aging-is-associated-with-impaired-angiogenesis-but-normal-microvascular-network-structure-in-the-rat-mesentery
#16
Richard S Sweat, David C Sloas, Scott A Stewart, Malwina Czarny-Ratajczak, Melody Baddoo, James R Eastwood, Ariana D Suarez-Martinez, Mohammad Sadegh Azimi, Hope E Burks, Lee O Chedister, Leann Myers, Walter Lee Murfee
A big problem associated with aging is thought to be impaired microvascular growth or angiogenesis. However, in order to link the evidence for impaired angiogenesis to microvascular dysfunction in aged tissues, we must compare adult versus aged microvascular networks in unstimulated scenarios. The objective of this study was to test the hypothesis that aged microvascular networks are characterized by both fewer vessels and the impaired ability to undergo angiogenesis. Mesentery tissues from adult (9 months) and aged (24 months) male Fischer 344 rats were harvested and immunolabeled for PECAM (an endothelial cell marker) according to two scenarios: unstimulated and stimulated...
November 18, 2016: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/27861625/computational-identification-of-tissue-specific-splicing-regulatory-elements-in-human-genes-from-rna-seq-data
#17
Eman Badr, Mahmoud ElHefnawi, Lenwood S Heath
Alternative splicing is a vital process for regulating gene expression and promoting proteomic diversity. It plays a key role in tissue-specific expressed genes. This specificity is mainly regulated by splicing factors that bind to specific sequences called splicing regulatory elements (SREs). Here, we report a genome-wide analysis to study alternative splicing on multiple tissues, including brain, heart, liver, and muscle. We propose a pipeline to identify differential exons across tissues and hence tissue-specific SREs...
2016: PloS One
https://www.readbyqxmd.com/read/27858497/high-fat-diet-and-exercise-lead-to-a-disrupted-and-pathogenic-dna-methylome-in-mouse-liver
#18
Dan Zhou, Ryan A Hlady, Marissa J Schafer, Thomas A White, Chen Liu, Jeong-Hyeon Choi, Jordan D Miller, Lewis R Roberts, Nathan K LeBrasseur, Keith D Robertson
High-fat diet consumption and sedentary lifestyle elevates risk for obesity, non-alcoholic fatty liver disease, and cancer. Exercise training conveys health benefits in populations with or without these chronic conditions. Diet and exercise regulate gene expression by mediating epigenetic mechanisms in many tissues; however, such effects are poorly documented in the liver, a central metabolic organ. To dissect the consequences of diet and exercise on the liver epigenome, we measured DNA methylation, using reduced representation bisulfite sequencing, and transcription, using RNA-seq, in mice maintained on a fast food diet with sedentary lifestyle or exercise, compared with control diet with and without exercise...
January 2, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27856250/ectopical-expression-of-fabp4-gene-can-induce-bovine-muscle-derived-stem-cells-adipogenesis
#19
Le Zhang, Yanfang Zhao, Yue Ning, Hongbao Wang, Linsen Zan
Fatty acid binding protein 4 (FABP4) plays a key role in Fatty acid catabolism in mammals. Findings from our previous studies have indicated that FABP4 neither affect the differentiation of bovine preadipocytes nor does it change the expression of upstream genes. To investigate whether ectopically expressed FABP4 can induces Muscle-Derived Stem Cells (MDSCs) lipid synthesis and understand the regulatory mechanism behind it. In this study, adenoviruses infection is achieved to ectopically expressed FABP4 in bovine MDSCs, RNA-seq analyses at the very early stages of induction were performed to reveal gene expression level changes during MDSCs transdifferentiation...
January 8, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27819726/association-between-a-non-synonymous-hsd17b4-single-nucleotide-polymorphism-and-meat-quality-traits-in-berkshire-pigs
#20
J L Jo, J H Hwang, S G Kwon, D H Park, T W Kim, D G Kang, G E Yu, I S Kim, J G Ha, C W Kim
Single nucleotide polymorphisms (SNPs) are useful genetic markers that allow correlation of genetic sequences with phenotypic traits. It is shown here that HSD17B4, a bifunctional enzyme mediating dehydrogenation and anhydration during β-oxidation of long-chain fatty acids, contains a non-synonymous SNP (nsSNP) of chr2:128,825,976A>G, c.2137A>G, I690V, within the sterol carrier protein-2 domain of the HSD17B4 gene, by RNA-Seq of liver RNA. The HSD17B4 mRNA was highly expressed in the kidney and liver among various other tissues in four pig breeds, namely, Berkshire, Duroc, Landrace, and Yorkshire...
November 3, 2016: Genetics and Molecular Research: GMR
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