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| Status |
Public on May 18, 2019 |
| Title |
Whole Transcriptome RNA-seq in Peromyscus maniculatus fibroblasts |
| Organism |
Peromyscus maniculatus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Analysis of gene expression can be challenging, especially if it involves genetically diverse populations that exhibit high variation in their individual expression profile. Despite this variation though, it is conceivable that in the same individuals a high degree of coordination is maintained between transcripts that belong to the same signaling modules and are associated with related biological functions. To explore this further, we calculated the correlation in the expression levels between each of ATF4, CHOP (DDIT3), GRP94, DNAJB9 (ERdj4), DNAJ3C (p58IPK) and HSPA5 (BiP/GRP78) with the whole transcriptome in primary fibroblasts from deer mice following induction of endoplasmic reticulum (ER) stress. Since these genes are associated with different transducers of the unfolded protein response (UPR) we postulated that their profile, in terms of correlation of transcripts, reflects distinct UPR branches engaged and therefore different biological processes. Standard gene ontology analysis was able to predict major functions associated with the corresponding transcript, and of the UPR arm related to that, namely regulation of the apoptotic response by ATF4 (PERK arm) and the ER stress associated degradation for GRP94 (IRE1). BiP, being a global regulator of the UPR, was associated with activation of ER stress in a rather global manner. Pairwise comparison in the correlation coefficients for these genes’ associated transcriptome showed the relevance of selected genes in terms of expression profiles.
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| Overall design |
Whole Transcriptome expression examination of Peromyscus transcriptome after induction of unfolded protein response
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| Contributor(s) |
Zhang Y, Havighorst A, Altomare D, Lucius M, Farmaki E, Chatzistamou I, Shtutman M, Kiaris H |
| Citation(s) |
31355672 |
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| Submission date |
May 17, 2019 |
| Last update date |
Aug 20, 2019 |
| Contact name |
Youwen Zhang |
| E-mail(s) |
youwen@email.sc.edu
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| Organization name |
University of South Carolina (Columbia)
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| Department |
Drug Discovery and Biomedical Sciences
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| Lab |
Dr. Hippokratis Kiaris
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| Street address |
715 Sumter Street CLS109
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| City |
Columbia |
| State/province |
South Carolina |
| ZIP/Postal code |
29208 |
| Country |
USA |
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| Platforms (1) |
| GPL26686 |
Illumina HiSeq 4000 (Peromyscus maniculatus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA543516 |
| SRA |
SRP198802 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE131429_20171118_DrHippokratis_CountsStrandSpecific2.csv.gz |
2.3 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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