A transcriptional landscape of 28 porcine tissues obtained by Super deepSAGE sequencing
| Autor: | Jun Yang, Zhou Guan, Mingjiang Xu, Tinghua Huang, Xiali Huang, Min Yang, Jinhui Liu, Kai Jin, Yu Deng, Rongxun Han, Kaihui Dong, Shijia Zhu, Wang Chen, Jun Yin, Zhi Chen, Min Yao |
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| Rok vydání: | 2020 |
| Předmět: |
Super deepSAGE
RUNX1 LPS lcsh:QH426-470 Swine lcsh:Biotechnology Sus scrofa Computational biology Biology Proteomics Deep sequencing 03 medical and health sciences 0302 clinical medicine Transcription (biology) lcsh:TP248.13-248.65 Gene expression Genetics Animals Gene Regulatory Networks Tissue Distribution Proto-Oncogene Proteins c-vav Transcription factor Gene 030304 developmental biology Regulation of gene expression 0303 health sciences Gene Expression Profiling PBMC Computational Biology Reproducibility of Results Toll-Like Receptor 2 lcsh:Genetics Gene Expression Regulation Lymphocyte Specific Protein Tyrosine Kinase p56(lck) 030220 oncology & carcinogenesis Core Binding Factor Alpha 2 Subunit Leukocytes Mononuclear DNA microarray Research Article Biotechnology |
| Zdroj: | BMC Genomics BMC Genomics, Vol 21, Iss 1, Pp 1-17 (2020) |
| DOI: | 10.21203/rs.2.24529/v1 |
| Popis: | Background Gene expression regulators identified in transcriptome profiling experiments may serve as ideal targets for genetic manipulations in farm animals. Results In this study, we developed a gene expression profile of 76,000+ unique transcripts for 224 porcine samples from 28 tissues collected from 32 animals using Super deepSAGE technology. Excellent sequencing depth was achieved for each multiplexed library, and replicated samples from the same tissues clustered together, demonstrating the high quality of Super deepSAGE data. Comparison with previous research indicated that our results not only have good reproducibility but also have greatly extended the coverage of the sample types as well as the number of genes. Clustering analysis revealed ten groups of genes showing distinct expression patterns among these samples. Our analysis of over-represented binding motifs identified 41 regulators, and we demonstrated a potential application of this dataset in infectious diseases and immune biology research by identifying an LPS-dependent transcription factor, runt-related transcription factor 1 (RUNX1), in peripheral blood mononuclear cells (PBMCs). The selected genes are specifically responsible for the transcription of toll-like receptor 2 (TLR2), lymphocyte-specific protein tyrosine kinase (LCK), and vav1 oncogene (VAV1), which belong to the T and B cell signaling pathways. Conclusions The Super deepSAGE technology and tissue-differential expression profiles are valuable resources for investigating the porcine gene expression regulation. The identified RUNX1 target genes belong to the T and B cell signaling pathways, making them novel potential targets for the diagnosis and therapy of bacterial infections and other immune disorders. |
| Databáze: | OpenAIRE |
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