Clc genomics workbench university of california

doi: 10.1016/j.gene.2015.09.026.Bagaza virus (BAGV), a member of the Ntaya serogroup in the Flavivirus genus of the Flaviviridae, was isolated from the brain tissue of a Himalayan monal pheasant that died following neurological signs in Pretoria, South Africa in 2016. Identification of novel alternative splicing transcript and expression analysis of bovine TMEM95 gene. Zhang S, Cai H, Yang Q, Shi T, Pan C, Lei C, et al. Global profiling of the gene expression and alternative splicing events during hypoxia-regulated chondrogenic differentiation in human cartilage endplate-derived stem cells. Yao Y, Shang J, Song W, Deng Q, Liu H, Zhou Y. RNA sequencing of cancer reveals novel splicing alterations. doi: 10.1038/nature09000.Д®swaran J, Horvath A, Godbole S, Reddy SD, Mudvari P, Ohshiro K, et al. 2017 46:582вЂ“92.Д«arash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, et al. Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. A broader knowledge about the functional attributes of these mRNA variants would be fundamental to elucidate the consequences of transcript diversity on the determinism of porcine phenotypes of economic interest.ДЄlternative splicing Differential expression Swine mRNA isoform. The increased levels of specific ITGA5, LITAF, TIMP1 and ANXA2 mRNA isoforms in HIGH pigs is consistent with reports indicating that the overexpression of these four genes is associated with obesity and metabolic disorders in humans.

Only five mRNA isoforms, produced by the ITGA5, SEMA4D, LITAF, TIMP1 and ANXA2 genes, remain significant after correction for multiple testing (q-value < 0.05 and вђ.6 log 2fold-change), being upregulated in HIGH pigs. By using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and вђ.6 log 2fold-change). Our analysis revealed that 10.9% of genes expressed in the GM muscle generate alternative mRNA isoforms, with an average of 2.9 transcripts per gene. In the current work, we have investigated the differential expression of mRNA isoforms in the gluteus medius (GM) muscle of 52 Duroc HIGH (increased backfat thickness, intramuscular fat and saturated and monounsaturated fatty acids contents) and LOW pigs (opposite phenotype, with an increased polyunsaturated fatty acids content). So far, the majority of porcine transcriptomic studies have investigated differences in gene expression at a global scale rather than at the mRNA isoform level. identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. 7 Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada. 6 Departament de CiГЁncia Animal i dels Aliments, Universitat AutГІnoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.

5 Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat AutГІnoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.

4 Departament de CiГЁncia Animal i dels Aliments, Universitat AutГІnoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.

3 Animal Breeding and Genetics Programme, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain.

2 CAPES Foundation, Ministry of Education of Brazil, Brasilia D.F, 70.040-020, Brazil.

1 Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat AutГІnoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.

Clc genomics workbench university of california