title: RNA-seq methods for identifying differentially expressed gene in human pancreatic islet cells treated with pro-inflammatory cytokines.
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.
authors.affiliation: Department of Endocrinology, Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.forename: Chang Long
authors.initials: CL
authors.lastname: Bi
authors.forename: Ning
authors.initials: N
authors.lastname: Lang
authors.forename: Yu Ze
authors.initials: YZ
authors.lastname: Li
authors.forename: Chao
authors.initials: C
authors.lastname: Xu
authors.forename: Ying Qi
authors.initials: YQ
authors.lastname: Zhang
authors.forename: Ai Xia
authors.initials: AX
authors.lastname: Zhai
authors.forename: Zhi Feng
authors.initials: ZF
authors.lastname: Cheng
mesh_terms: D019295:Computational Biology / Q000379:methods; D016207:Cytokines / Q000494:pharmacology*; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D018836:Inflammation Mediators / Q000494:pharmacology*; D050417:Insulin-Secreting Cells / Q000187:drug effects* / Q000378:metabolism*; D007515:Islets of Langerhans / Q000166:cytology*; D062085:RNA, Long Noncoding; D017423:Sequence Analysis, RNA
chemical_list: D016207:Cytokines; D018836:Inflammation Mediators; D062085:RNA, Long Noncoding