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10.1142/S0219720015500109

http://scihub22266oqcxt.onion/10.1142/S0219720015500109
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suck abstract from ncbi


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pmid25708305
      J+Bioinform+Comput+Biol 2015 ; 13 (2 ): 1550010
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  • Analytical workflow profiling gene expression in murine macrophages #MMPMID25708305
  • Nixon SE ; González-Peña D ; Lawson MA ; McCusker RH ; Hernandez AG ; O'Connor JC ; Dantzer R ; Kelley KW ; Rodriguez-Zas SL
  • J Bioinform Comput Biol 2015[Apr]; 13 (2 ): 1550010 PMID25708305 show ga
  • Comprehensive and simultaneous analysis of all genes in a biological sample is a capability of RNA-Seq technology. Analysis of the entire transcriptome benefits from summarization of genes at the functional level. As a cellular response of interest not previously explored with RNA-Seq, peritoneal macrophages from mice under two conditions (control and immunologically challenged) were analyzed for gene expression differences. Quantification of individual transcripts modeled RNA-Seq read distribution and uncertainty (using a Beta Negative Binomial distribution), then tested for differential transcript expression (False Discovery Rate-adjusted p-value < 0.05). Enrichment of functional categories utilized the list of differentially expressed genes. A total of 2079 differentially expressed transcripts representing 1884 genes were detected. Enrichment of 92 categories from Gene Ontology Biological Processes and Molecular Functions, and KEGG pathways were grouped into 6 clusters. Clusters included defense and inflammatory response (Enrichment Score = 11.24) and ribosomal activity (Enrichment Score = 17.89). Our work provides a context to the fine detail of individual gene expression differences in murine peritoneal macrophages during immunological challenge with high throughput RNA-Seq.
  • |Animals [MESH]
  • |Computational Biology [MESH]
  • |Gene Expression Profiling/*statistics & numerical data [MESH]
  • |Gene Ontology/statistics & numerical data [MESH]
  • |Macrophages, Peritoneal/immunology/*metabolism [MESH]
  • |Male [MESH]
  • |Mice [MESH]
  • |Mice, Inbred C57BL [MESH]
  • |Sequence Analysis, RNA/statistics & numerical data [MESH]


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