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Classification and functional identification by gene expression patterns from various muscle tissues in a single livestock

ABSTRACT: Purpose : The RNA-seq data of 18 skeletal muscle tissues obtained from one Jejunal were sequenced. In this study, we aimed to group multiple tissues by unsupervised clustering of tissues based on expression pattern alone, and to find the criteria for dividing the classified tissues and the causative genes. Method : The raw counts obtained from the STAR 2 pass alignment were obtained. The log2 normalization value of raw counts of each sample is classified by hierarchical clustering. The eighteen samples were classified into two groups of nine each. Differential expression analysis of each group through R package DESeq2 revealed a total of 1104 Differentially expressed genes (DEGs). Result and Conclusion : Based on myosin heavy chain family gene expression in Identified DEGs, the criteria for dividing the two groups were determined by the classification of slow-twitch and fast-twitch muscle according to the content of myosin heavy chain fiber. ?In addition, we confirmed the up-regulation of the genes that are characteristic of the slow-twitch muscle, and identified that the central genes that express these features play a role in maintaining cardiovascular homeostasis.

ORGANISM(S): Equus caballus

PROVIDER: GSE113147 | GEO | 2020/11/17

REPOSITORIES: GEO

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Project description:The zebrafish u-boot (ubo) gene encodes the transcription factor Prdm1, which is essential for the specification of the primary slow twitch muscle fibres that derive from adaxial cells. Here we show that Prdm1 executes this function by acting as a transcriptional repressor. Expression of the slow twitch isoform of the myosin heavy chain in adaxial cells is achieved by Prdm1 mediated repression of the transcriptional repressor Sox6. Using Chromatin immuno precipitation (ChIP) we found that genes encoding fast specific isoforms of sarcomeric proteins are direct targets of Prdm1. These genes are ectopically expressed in the adaxial cells of ubotp39 mutant embryos, suggesting that Prdm1 promotes slow twitch fibre differentiation by acting both as a global repressor of fast fibre specific genes as well as of a repressor of slow specific genes. Keywords: ChIP-chip Genomic array design. Microarrays were designed as described below and manufactured by Agilent Technologies (www.agilent.com). We have previously described the ChIP-chip technique in zebrafish and the design of promoter microarrays which cover a 2kb region around the transcription start sites (TSSs) of 11,512 zebrafish genes based on Zv4 (Wardle et al, 2006. Genome Biology 7:R71). In order to capture additional regulatory information further from the basal promoter region we also designed an expanded set of 60mer probes that cover 9kb upstream and 3kb downstream of the TSS of these genes using the same parameters as for the 2kb microarrays. These probe sequences were re-mapped to Zv6 over the course of the project and the coordinates given are for Zv6. We also incorporated several sets of control probes, both positive and negative. On each array there are 769 negative probes designed against zebrafish gene desert regions and Arabidopsis thaliana genes. In addition we included duplicates of promoter probes for several genes that we anticipated may be bound by factors of interest for this and other studies (tnnt3a, mylz2, myhz2, wnt11, flh, vent, msgn1, myod, fgf8, pcdh8) and these probes are arrayed on both slides slide. Finally on each array there are 1804 controls added by Agilent. The final design contained 352,490 probes divided between two microarray slides. Further information on design and manufacture of the microarrays can be found at the Agilent Technologies website.

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Classification and functional identification by gene expression patterns from various muscle tissues in a single livestock

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