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muscle RNA-seq

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https://www.readbyqxmd.com/read/28428068/comparative-analysis-of-gene-expression-profiles-for-several-migrating-cell-types-identifies-cell-migration-regulators
#1
Young-Kyung Bae, Frank Macabenta, Heather Leigh Curtis, Angelike Stathopoulos
Cell migration is an instrumental process that ensures cells are properly positioned to support the specification of distinct tissue types during development. To provide insight, we used fluorescence activated cell sorting (FACS) to isolate two migrating cell types from the Drosophila embryo: caudal visceral mesoderm (CVM) cells, precursors of longitudinal muscles of the gut, and hemocytes (HCs), the Drosophila equivalent of blood cells. ~350 genes were identified from each of the sorted samples using RNA-seq, and in situ hybridization was used to confirm expression within each cell type or, alternatively, within other interacting, co-sorted cell types...
April 17, 2017: Mechanisms of Development
https://www.readbyqxmd.com/read/28424332/improving-genetic-diagnosis-in-mendelian-disease-with-transcriptome-sequencing
#2
Beryl B Cummings, Jamie L Marshall, Taru Tukiainen, Monkol Lek, Sandra Donkervoort, A Reghan Foley, Veronique Bolduc, Leigh B Waddell, Sarah A Sandaradura, Gina L O'Grady, Elicia Estrella, Hemakumar M Reddy, Fengmei Zhao, Ben Weisburd, Konrad J Karczewski, Anne H O'Donnell-Luria, Daniel Birnbaum, Anna Sarkozy, Ying Hu, Hernan Gonorazky, Kristl Claeys, Himanshu Joshi, Adam Bournazos, Emily C Oates, Roula Ghaoui, Mark R Davis, Nigel G Laing, Ana Topf, Peter B Kang, Alan H Beggs, Kathryn N North, Volker Straub, James J Dowling, Francesco Muntoni, Nigel F Clarke, Sandra T Cooper, Carsten G Bönnemann, Daniel G MacArthur
Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples...
April 19, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28413781/sequencing-and-de-novo-transcriptome-assembly-of-the-chinese-giant-salamander-andrias-davidianus
#3
Yong Huang, Xiao Chan Gao, Jian Li Xiong, Hong Tao Ren, Xi Hong Sun
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we obtained the RNA-Seq data from a pool of A. davidianus tissue including spleen, liver, muscle, kidney, skin, testis, gut and heart using Illumina HiSeq 2500 platform. A total of 15,398,997,600 bp were obtained, corresponding to 102,659,984 raw reads...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28408205/temporal-spatial-and-phenotypical-changes-of-pdgfr%C3%AE-expressing-fibroblasts-during-late-lung-development
#4
Mehari Endale, Shawn Ahlfeld, Erik Bao, Xiaoting Chen, Jenna Green, Zach Bess, Matthew T Weirauch, Yan Xu, Anne Karina Perl
Many studies have investigated the source and role of epithelial progenitors during lung development; such information is limited for fibroblast populations and their complex role in the developing lung. In this study, we characterized the spatial location, mRNA expression and Immunophenotyping of PDGFRα(+) fibroblasts during sacculation and alveolarization. Confocal microscopy identified spatial association of PDGFRα expressing fibroblasts with proximal epithelial cells of the branching bronchioles and the dilating acinar tubules at E16...
April 11, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28404879/developmental-transcriptome-profiling-of-bovine-muscle-tissue-reveals-an-abundant-gosb-that-regulates-myoblast-proliferation-and-apoptosis
#5
Hui Li, Xuefeng Wei, Jiameng Yang, Dong Dong, Yongzhen Huang, Xianyong Lan, Martin Plath, Chuzhao Lei, Xinglei Qi, Yueyu Bai, Hong Chen
The formation of bovine skeletal muscle involves complex developmental and physiological processes that play a vital role in determining the quality of beef; however, the regulatory mechanisms underlying differences in meat quality are largely unknown. We conducted transcriptome analysis of bovine muscle tissues to compare gene expression profiles between embryonic and adult stages. Total RNAs from skeletal muscle of Qinchuan cattle at fetal and adult stages were used to construct libraries for Illumina next-generation sequencing using the Ribo-Zero RNA sequencing (RNA-Seq) method...
March 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28400270/differential-expression-profile-of-mirnas-in-porcine-muscle-and-adipose-tissue-during-development
#6
Qi Wang, Renli Qi, Jing Wang, Wenming Huang, Yongjiang Wu, Huang Xiaofeng, Feiyun Yang, Jinxiu Huang
MicroRNAs (miRNAs) are a class of non-coding RNAs that play a crucial regulatory role in many biological processes. Previous studies have reported miRNAs that are associated with the growth, differentiation, and proliferation of myocytes and adipocytes in pigs. However, differences in the miRNA expression profiles between muscle and adipose tissues during porcine development are unknown. Muscle and adipose tissues are the two major organs that are crucial for dynamic energy balance in the development and metabolism...
April 8, 2017: Gene
https://www.readbyqxmd.com/read/28381300/linkages-between-changes-in-the-3d-organization-of-the-genome-and-transcription-during-myotube-differentiation-in-vitro
#7
Malina D Doynova, James F Markworth, David Cameron-Smith, Mark H Vickers, Justin M O'Sullivan
BACKGROUND: The spatial organization of eukaryotic genomes facilitates and reflects the underlying nuclear processes that are occurring in the cell. As such, the spatial organization of a genome represents a window on the genome biology that enables analysis of the nuclear regulatory processes that contribute to mammalian development. METHODS: In this study, Hi-C and RNA-seq were used to capture the genome organization and transcriptome in mouse muscle progenitor cells (C2C12 myoblasts) before and after differentiation to myotubes, in the presence or absence of the cytidine analogue AraC...
April 5, 2017: Skeletal Muscle
https://www.readbyqxmd.com/read/28380516/integrated-analysis-of-non-coding-rna-and-mrna-expression-profiles-of-2-pig-breeds-differing-in-muscle-traits
#8
J Sun, M Xie, Z Huang, H Li, T Chen, R Sun, J Wang, Qianyun Xi, T Wu, Y Zhang
Production of high-quality meat is important to satisfy the consumer and allow the pork industry to be competitive. It is evident that different muscle fiber types in different breeds greatly influence the pork quality, but the underlying molecular mechanism remains unclear. We used Ribo-Zero RNA-Seq and miRNA-Seq to examine global expressions of protein-coding transcripts and non-coding RNAs including miRNA, lncRNA, and circRNA in the longissimus dorsi of Landrace and Lantang pigs. Of the 22,469 identified coding transcripts, only 547 candidates were differentially expressed, including 461 upregulated and 86 downregulated transcripts in the Lantang pigs compared with Landrace...
March 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28379566/lncfunnet-an-integrated-computational-framework-for-identification-of-functional-long-noncoding-rnas-in-mouse-skeletal-muscle-cells
#9
Jiajian Zhou, Suyang Zhang, Huating Wang, Hao Sun
Long noncoding RNAs (lncRNAs) are key regulators of diverse cellular processes. Recent advances in high-throughput sequencing have allowed for an unprecedented discovery of novel lncRNAs. To identify functional lncRNAs from thousands of candidates for further functional validation is still a challenging task. Here, we present a novel computational framework, lncFunNet (lncRNA Functional inference through integrated Network) that integrates ChIP-seq, CLIP-seq and RNA-seq data to predict, prioritize and annotate lncRNA functions...
April 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28375666/glucocorticoid-receptor-chip-seq-identifies-plcd1-as-a-klf15-target-that-represses-airway-smooth-muscle-hypertrophy
#10
Sarah K Sasse, Vineela Kadiyala, Thomas Danhorn, Reynold A Panettieri, Tzu L Phang, Anthony N Gerber
Glucocorticoids exert important therapeutic effects on airway smooth muscle (ASM), yet few direct targets of glucocorticoid signaling in ASM have been definitively identified. Here, we show that the transcription factor, KLF15, is directly induced by glucocorticoids in primary human ASM and that KLF15 represses ASM hypertrophy. We integrated transcriptome data from KLF15 overexpression with genome-wide analysis of RNA Polymerase II (RNAPII) and glucocorticoid receptor (GR) occupancy (i.e. ChIP-seq) to identify PLCD1 as both a KLF15-regulated gene and a novel repressor of ASM hypertrophy...
April 4, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28365159/genetic-alterations-in-the-molecular-subtypes-of-bladder-cancer-illustration-in-the-cancer-genome-atlas-dataset
#11
REVIEW
Woonyoung Choi, Andrea Ochoa, David J McConkey, Mattias Aine, Mattias Höglund, William Y Kim, Francisco X Real, Anne E Kiltie, Ian Milsom, Lars Dyrskjøt, Seth P Lerner
CONTEXT: Recent whole genome mRNA expression profiling studies revealed that bladder cancers can be grouped into molecular subtypes, some of which share clinical properties and gene expression patterns with the intrinsic subtypes of breast cancer and the molecular subtypes found in other solid tumors. The molecular subtypes in other solid tumors are enriched with specific mutations and copy number aberrations that are thought to underlie their distinct progression patterns, and biological and clinical properties...
March 29, 2017: European Urology
https://www.readbyqxmd.com/read/28357642/genome-wide-gene-expression-profiling-of-tongue-squamous-cell-carcinoma-by-rna-seq
#12
Hai Xia Zhang, Ou Sheng Liu, Chao Deng, Yan He, Ye Qian Feng, Jin An Ma, Chun Hong Hu, Zhan Gui Tang
OBJECTIVE: Tongue squamous cell carcinoma (TSCC) is significantly more malignant than other type of oral squamous cell carcinoma (OSCC). In this study, we aimed to identify specific global gene expression signatures of TSCC to investigate the more invasive behavior of the deeply infiltrating cancer. METHODS: Using RNA-seq technology, we detected gene expression of 20 TSCCs, 20 matched paratumor tissues, and 10 healthy normal mucosa tissues. Enrichment analysis of gene ontology (GO) and pathway was conducted using online tools DAVID for the dysregulated genes...
March 29, 2017: Clinical Oral Investigations
https://www.readbyqxmd.com/read/28350389/erratum-targeted-rna-seq-profiling-of-splicing-pattern-in-the-dmd-gene-exons-are-mostly-constitutively-spliced-in-human-skeletal-muscle
#13
Anne-Laure Bougé, Eva Murauer, Emmanuelle Beyne, Julie Miro, Jessica Varilh, Magali Taulan, Michel Koenig, Mireille Claustres, Sylvie Tuffery-Giraud
No abstract text is available yet for this article.
March 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28340271/snp-detection-using-rna-sequences-of-candidate-genes-associated-with-puberty-in-cattle
#14
M M Dias, A Cánovas, C Mantilla-Rojas, D G Riley, P Luna-Nevarez, S J Coleman, S E Speidel, R M Enns, A Islas-Trejo, J F Medrano, S S Moore, M R S Fortes, L T Nguyen, B Venus, I S D P Diaz, F R P Souza, L F S Fonseca, F Baldi, L G Albuquerque, M G Thomas, H N Oliveira
Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28338730/genetic-variability-of-the-activity-of-bidirectional-promoters-a-pilot-study-in-bovine-muscle
#15
Cédric Meersseman, Rabia Letaief, Véronique Léjard, Emmanuelle Rebours, Gabriel Guillocheau, Diane Esquerré, Anis Djari, Amanda Chamberlain, Christy Vander Jagt, Christophe Klopp, Mekki Boussaha, Gilles Renand, Abderrahman Maftah, Daniel Petit, Dominique Rocha
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters...
February 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28330496/calcium-dysregulation-functional-calpainopathy-and-endoplasmic-reticulum-stress-in-sporadic-inclusion-body-myositis
#16
David R Amici, Iago Pinal-Fernandez, Davi A G Mázala, Thomas E Lloyd, Andrea M Corse, Lisa Christopher-Stine, Andrew L Mammen, Eva R Chin
Sporadic inclusion body myositis (IBM) is the most common primary myopathy in the elderly, but its pathoetiology is still unclear. Perturbed myocellular calcium (Ca(2+)) homeostasis can exacerbate many of the factors proposed to mediate muscle degeneration in IBM, such as mitochondrial dysfunction, protein aggregation, and endoplasmic reticulum stress. Ca(2+) dysregulation may plausibly be initiated in IBM by immune-mediated membrane damage and/or abnormally accumulating proteins, but no studies to date have investigated Ca(2+) regulation in IBM patients...
March 22, 2017: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/28329397/resveratrol-improves-vascular-function-and-mitochondrial-number-but-not-glucose-metabolism-in-older-adults
#17
Rena M Pollack, Nir Barzilai, Valentin Anghel, Ameya S Kulkarni, Aaron Golden, Pilib O'Broin, David A Sinclair, Michael S Bonkowski, Alexander J Coleville, Danielle Powell, Sharon Kim, Ruin Moaddel, Daniel Stein, Kehao Zhang, Meredith Hawkins, Jill P Crandall
Background: Resveratrol, a plant-derived polyphenol, has been reported to improve glucose metabolism and vascular function and to extend life span in animal models, but studies in humans have been inconclusive. Methods: In a randomized, double-blind crossover study, we treated older glucose-intolerant adults (n = 30) with resveratrol (2-3 g/daily) or placebo, each for 6 weeks. A standard mixed-meal test was used to assess insulin sensitivity (Matsuda index) and secretion (C-peptide deconvolution) and vascular function by reactive hyperemia peripheral arterial tonometry...
March 16, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28321693/age-at-diagnosis-obesity-smoking-and-molecular-subtypes-in-muscle-invasive-bladder-cancer
#18
Xuezheng Sun, Katherine A Hoadley, William Y Kim, Helena Furberg, Andrew F Olshan, Melissa A Troester
BACKGROUND: Heterogeneity of muscle-invasive bladder cancer (MIBC) has been characterized using whole-genome mRNA expression data, showing distinct molecular and clinicopathological characteristics by subtypes. However, associations between risk factors and molecular subtypes have not been reported. METHODS: Four previously published schemes were used to categorize molecular subtypes in 372 MIBC patients from the Cancer Genome Atlas (TCGA). Data on gene expression (RNA-seq), demographic, and clinicopathological characteristics were retrieved through TCGA data portal...
March 20, 2017: Cancer Causes & Control: CCC
https://www.readbyqxmd.com/read/28286175/cilia-dependent-gli-processing-in-neural-crest-cells-is-required-for-tongue-development
#19
Grethel Millington, Kelsey H Elliott, Ya-Ting Chang, Ching-Fang Chang, Andrzej Dlugosz, Samantha A Brugmann
Ciliopathies are a class of diseases caused by the loss of a ubiquitous, microtubule-based organelle called a primary cilium. Ciliopathies commonly result in defective development of the craniofacial complex, causing midfacial defects, craniosynostosis, micrognathia and aglossia. Herein, we explored how the conditional loss of primary cilia on neural crest cells (Kif3a(f/f);Wnt1-Cre) generated aglossia. On a cellular level, our data revealed that aglossia in Kif3a(f/f);Wnt1-Cre embryos was due to a loss of mesoderm-derived muscle precursors migrating into and surviving in the tongue anlage...
March 9, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28283548/smooth-muscle-cell-specific-deletion-of-col15a1-unexpectedly-leads-to-impaired-development-of-advanced-atherosclerotic-lesions
#20
Brittany G Durgin, Olga A Cherepanova, Delphine Gomez, Themistoclis Karaoli, Gabriel F Alencar, Joshua T Butcher, Yu-Qing Zhou, Michelle P Bendeck, Brant E Isakson, Gary K Owens, Jessica J Connelly
Atherosclerotic plaque rupture with subsequent embolic events is a major cause of sudden death from myocardial infarction or stroke. Although smooth muscle cells (SMC) produce and respond to collagens in vitro, there is no direct evidence in vivo that SMC are a crucial source of collagens and that this impacts lesion development or fibrous cap formation. We sought to determine how conditional SMC specific knockout of collagen type XV (COL15A1) in SMC lineage tracing mice affects advanced lesion formation given: 1) we previously identified a Col15a1 sequence variant associated with age related atherosclerosis; 2) COL15A1 is a matrix organizer enhancing tissue structural integrity; and 3) siRNA mediated Col15a1 knockdown increased migration and decreased proliferation of cultured human SMC...
March 10, 2017: American Journal of Physiology. Heart and Circulatory Physiology
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