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| Status |
Public on Oct 22, 2019 |
| Title |
BRIN-BD11 pancreatic beta cell mRNA profile upon treatment with Class1 HDAC inhibitor MS-275 |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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.
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| Overall design |
Effect of Class1 HDAC inhibitor MS-275 on BRIN-BD11 pancreatic beta cell transcriptome
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| Contributor(s) |
Mitra P, Bele S, Mutha NV, Katika MR |
| Citation missing |
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| |
| Submission date |
Oct 21, 2019 |
| Last update date |
Oct 24, 2019 |
| Contact name |
PRASENJIT MITRA |
| E-mail(s) |
prasenjit.mitra01604@gmail.com
|
| Phone |
04066571526
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| Organization name |
Dr.Reddy’s Institute of Life Sciences
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| Street address |
University of Hyderabad Campus, Gachibowli
|
| City |
Hyderabad |
| State/province |
Telangana |
| ZIP/Postal code |
500032 |
| Country |
India |
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| Platforms (1) |
| GPL25947 |
Illumina NovaSeq 6000 (Rattus norvegicus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA578636 |
| SRA |
SRP226423 |
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