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RNA-seq methods for identifying differentially expressed gene in human pancreatic islet cells treated with pro-inflammatory cytokines

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Abstract

Type 1 diabetes is a chronic autoimmune disease in which pancreatic beta cells are killed by the infiltrating immune cells as well as the cytokines released by these cells. Many studies indicate that inflammatory mediators have an essential role in this disease. In the present study, we profiled the transcriptome in human islets of langerhans under control conditions or following exposure to the pro-inflammatory cytokines based on the RNA sequencing dataset downloaded from SRA database. After filtered the low-quality ones, the RNA readers was aligned to human genome hg19 by TopHat and then assembled by Cufflinks. The expression value of each transcript was calculated and consequently differentially expressed genes were screened out. Finally, a total of 63 differentially expressed genes were identified including 60 up-regulated and three down-regulated genes. GBP5 and CXCL9 stood out as the top two most up-regulated genes in cytokines treated samples with the log2 fold change of 12.208 and 10.901, respectively. Meanwhile, PTF1A and REG3G were identified as the top two most down-regulated genes with the log2 fold change of −3.759 and −3.606, respectively. Of note, we also found 262 lncRNAs (long non-coding RNA), 177 of which were inferred as novel lncRNAs. Further in-depth follow-up analysis of the transcriptional regulation reported in this study may shed light on the specific function of these lncRNA.

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Acknowledgments

This work was funded by grants from the Foundation of Heilongjiang Provincial Education Department of China (12531319, 11551238), Foundation of Heilongjiang Provincial Health Department of China (2009-181, 2009-207, 2012-715), Foundation of Heilongjiang Provincial Postdoctor of China (LBH-Z11086). We wish to express our warm thanks to Fenghe (Shanghai) Information Technology Co., Ltd. Their ideas and help gave a valuable added dimension to our research.

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Authors and Affiliations

  1. Department of Endocrinology, Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China

    Bo Li, Chang Long Bi, Ning Lang, Chao Xu, Ying Qi Zhang & Zhi Feng Cheng

  2. Department of the Fourth Internal Medicine, Heilongjiang Province Tuberculosis Control Center, Harbin, 150500, China

    Yu Ze Li

  3. Department of Microbiology, Harbin Medical University, Harbin, 150081, China

    Ai Xia Zhai

  4. Heilongjiang Provincial Science and Technology Innovation Team in Higher Education Institutes for Infection and Immunity, Harbin Medical University, Harbin, 150081, China

    Ai Xia Zhai

  5. Heilongjiang Provincial Key Laboratory for Infection and Immunity, Harbin Medical University, Harbin, 150081, China

    Ai Xia Zhai

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  1. Bo Li
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  3. Ning Lang
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  4. Yu Ze Li
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Correspondence to Ying Qi Zhang, Ai Xia Zhai or Zhi Feng Cheng.

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Bo Li, Chang Long Bi and Ning Lang are co-first authors in this study.

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Li, B., Bi, C.L., Lang, N. et al. RNA-seq methods for identifying differentially expressed gene in human pancreatic islet cells treated with pro-inflammatory cytokines. Mol Biol Rep 41, 1917–1925 (2014). https://doi.org/10.1007/s11033-013-3016-2

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