 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 29, 2019 |
| Title |
Comparison of gene expression in the long-lived hsb-1 mutant and hsf-1 overexpression C. elegans strains |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: We used RNA-Seq to compare the gene expression profiles in two long-lived C. elegans strains: (1) animals with a loss-of-function mutation in the hsb-1 gene, and (2) animals overexpressing hsf-1 under its endogenous promoter. Previous studies indicated that life span extension in both these strains is hsf-1-dependent.
Methods: mRNA-Seq profiles for three biological replicates each of day 1 adult wild-type (N2 strain), hsb-1 mutant and hsf-1 overexpression strains were generated using 50 bp single-end sequencing on an Illumina HiSeq 2500 platform. The sequencing reads that passed quality control were aligned to the C. elegans reference transcriptome (WS220 release) using Bowtie 2 and splicing junctions were mapped using TopHat. Cufflinks was used to calculate FPKM values and CuffDiff 2 was used to identify differentially expressed genes based on the following two criteria: false discovery rate (FDR)-adjusted p value < 0.05 and fold-change ≥ 1.5.
Results: Using our mRNA-Seq workflow, we mapped at least 14 million reads per sample to the C. elegans transcriptome at greater than 96 percent alignment rate for the raw reads. Expression of 7,478 genes was found to be significantly altered in the hsf-1 overexpression strain relative to wild-type worms, while only 1,855 genes had singnificantly different expression in the hsb-1 mutant strain relative to wild-type. Using our criterion of ≥ 1.5-fold change in gene expression, we found 1,820 and 662 genes to be differentially expressed relative to wild-type in hsf-1 overexpression and hsb-1 mutant strains, respectively. The 247 genes that were differentially expressed in both hsf-1 overexpression and hsb-1 mutant strains showed a strongly correlated expression pattern in the two strains.
Conclusions: hsf-1 overexpression induces global transcriptional suppression in C. elegans. Genetic ablation of hsb-1 produces similar life span extension in worms as hsf-1 overexpression, but alters expression of a much smaller subset of the C. elegans transcriptome. Hence, HSB-1 is a specific regulator of the transactivation potential of HSF-1 that selectively modulates gene expression relevant to longevity determination in worms.
|
| |
|
| Overall design |
Whole animal mRNA profiles of day 1 adult wild-type (N2 strain), hsb-1 mutant and hsf-1 overexpression strains were generated, in triplicates, using 50 bp single-end sequencing on an Illumina HiSeq 2500 platform.
|
| |
|
| Contributor(s) |
McEachin R, Surojit S, Hsu A |
| Citation(s) |
30894454 |
| |
| Submission date |
Sep 14, 2018 |
| Last update date |
May 29, 2019 |
| Contact name |
Richard C McEachin |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Department |
DCM&B
|
| Street address |
2800 Plymouth Road
|
| City |
Ann Arbor |
| State/province |
United States |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL18245 |
Illumina HiSeq 2500 (Caenorhabditis elegans) |
|
| Samples (9)
|
|
| Relations |
| BioProject |
PRJNA491191 |
| SRA |
SRP161795 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE119993_CuffDiff_rawCountsMatrix.txt.gz |
520.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...