Ontology highlight
ABSTRACT:
PROVIDER: PRJNA637679 | ENA |
REPOSITORIES: ENA
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2024-02-08 | PXD049451 | iProX
Project description:Methods: We performed mRNA sequence analysis by deep sequencing, in triplicate, using Illumina HiSeq to assess the impact of Class1 HDAC inhibitor MS-275 in regulating gene expression in BRIN-BD11 pancreatic beta cells. The transcriptome libraries were constructed using the NEB adapters and were sequenced on at 150 nucleotide read length using the paired-end chemistry. The raw reads were subjected to Adapter and low quality reads removal by Trimmomatic -0.36v. The sequence reads that passed quality filters was mapped to the Rattus_norvegicus Rnor_6.0 using STAR , counted using feature count module of sub reads package and was normalized in DESeq2-3. Differentially expressed genes were selected based on log2-ratio change with p-value <0.05 (Student‘s t test, unpaired). Hierarchical clustering was performed with the programs Cluster (uncentered correlation; average linkage clustering) and Treeview. Results: We mapped 136,002,940 (136 million reads) reads per sample to rat genome (Rnor_6.0) and observed 97% alignment to the reference rat genome. We found that 1858 genes were up regulated and 624 genes got down regulated on MS-275 treatment (log fold change ≥±2 p value < 0.05). Inference: Gene ontology reveals that the upregulated pathways upon MS-275 treatment include endocytosis, cAMP signaling, insulin secretion, Wnt signaling PI3K-Akt signaling and thermogenesis while the downregulated genes include histone modification, chromosome organization and cell cycle regulation. The study represents first detailed mRNA profiling of BRIN-BD11 pancreatic beta cell in context of modulation of expression upon treatment with Class1 HDAC inhibitor MS-275.
2019-10-22 | GSE139147 | GEO
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