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Series GSE112511 Query DataSets for GSE112511
Status Public on Dec 30, 2018
Title RNA-seq Analysis of Transcriptomes in β-Gal-overexpressing, NIK-overexpressing, and NIK(KA)-overexpressing αTC1-6 cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goal of this study is to determine the molecular mechanisms involved in the NIK regulation of α cell function.
Methods: mRNA profiles of β-Gal control, NIK, and NIK(KA) overexpressed αTC1-6 cells were generated by deep sequencing using an Illumina Hiseq platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.89) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1).
Conclusion: Our study represents the first detailed analysis of NIK-overexpressing aTC1-6 cell transcriptomes, generated by RNA-seq technology. Our results show that 328 genes were upregulated and 48 genes were downregulated following NIK overexpression. GO analysis indicated that the upregulated genes were primarily related to the immune response. KEGG pathway enrichment analysis showed that immune signaling pathways, including the TNF, NF-κB, and chemokine signaling pathways, were significantly activated by NIK overexpression in aTC1-6 cells, while genes related to metabolism-associated signal pathways were significantly decreased. NIK(KA), the dominant-negative mutant of NIK, does not affect gene expression in aTC1-6 cells.
Overall design mRNA profiles of β-Gal control, NIK, and NIK(KA) overexpression αTC1-6 cells were generated by deep sequencing, in a single test, using Illumina
Contributor(s) Chen Z, Li X
Citation(s) 30613274
Submission date Mar 29, 2018
Last update date Apr 19, 2019
Contact name Zheng Chen
Phone +8645186402029
Organization name Harbin Institute of Technology
Street address 92 Xidazhijie Harbin Institute of Technology
City Harbin
State/province Heilongjiang
ZIP/Postal code 150001
Country China
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (3)
GSM3071963 β-Gal control αTC1-6 cells
GSM3071964 NIK overexpression αTC1-6 cells
GSM3259679 NIK(KA)
BioProject PRJNA448031
SRA SRP136755

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Supplementary file Size Download File type/resource
GSE112511_RAW.tar 3.5 Mb (http)(custom) TAR (of XLSX)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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