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| Status |
Public on Oct 22, 2024 |
| Title |
Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically-diverse Caenorhabditis nematodes. |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We present a survey of longevity effects for compounds suggested by a previously published computational prediction set using the comprehensive, multi-species approach utilized by the Caenorhabditis Intervention Testing Program (CITP). The compound all-trans retinoic acid extended lifespan in the nematode Caenorhabditis elegans. Given the dependency of lifespan extension under atRA treatment, we used RNA-seq to assess transcriptional changes under atRA treatment in wildtype N2 animals. In order to further dissect transcriptional response in detail, we repeated our transcriptional analysis in hsf-1(sy441) and aak-2(ok524) mutants.
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| Overall design |
We performed differential gene expression analysis comparing atRA-treated and DMSO control samples (4 biological replicates each) in 4 day old adult worms in the wildtype N2, PS3551 [hsf-1(sy411)], and RB754 [aak-2(ok524)] strains.
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| Web link |
https://www.doi.org/10.7554/eLife.104375
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| Contributor(s) |
Banse SA, Sedore CA, Coleman-Hulbert AL, Johnson E, Onken B, Hall D, Segerdell E, Jones EG, Song Y, Osman H, Xue J, Battistoni E, Guo S, Foulger AC, Achanta M, Sheikh M, Fitzgibbon T, Willis JH, Woodruff GC, Driscoll M, Lithgow G, Phillips PC |
| Citation missing |
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| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| U01 AG045844 |
Caenorhabditis Intervention Testing Program - Buck Institute |
BUCK INSTITUTE FOR RESEARCH ON AGING |
Gordon J Lithgow |
| U01 AG045864 |
Caenorhabditis Intervention Testing Program: Interventions That Modulate Health, Longevity and Aging Hallmarks |
RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY |
Monica A. Driscoll |
| U01 AG045829 |
Caenorhabditis Intervention Testing Program at Oregon |
UNIVERSITY OF OREGON |
Patrick C. Phillips |
| U24 AG056052 |
Caenorhabditis Testing Program Data Coordinating Center |
UNIVERSITY OF OREGON |
Patrick C. Phillips |
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| Submission date |
Jul 18, 2024 |
| Last update date |
Jan 22, 2025 |
| Contact name |
Patrick Phillips |
| Organization name |
University of Oregon
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| Department |
Institute of Ecology and Evolution
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| Street address |
5289 University of Oregon
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| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403-5289 |
| Country |
USA |
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| Platforms (1) |
| GPL22765 |
Illumina HiSeq 4000 (Caenorhabditis elegans) |
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| Samples (24)
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| GSM8404215 |
N2 worms, atRA, rep 4 |
| GSM8404216 |
N2 worms, DMSO, rep 1 |
| GSM8404217 |
N2 worms, DMSO, rep 2 |
| GSM8404218 |
N2 worms, DMSO, rep 3 |
| GSM8404219 |
N2 worms, DMSO, rep 4 |
| GSM8404220 |
PS3551 worms, atRA, rep 1 |
| GSM8404221 |
PS3551 worms, atRA, rep 2 |
| GSM8404222 |
PS3551 worms, atRA, rep 3 |
| GSM8404223 |
PS3551 worms, atRA, rep 4 |
| GSM8404224 |
PS3551 worms, DMSO, rep 1 |
| GSM8404225 |
PS3551 worms, DMSO, rep 2 |
| GSM8404226 |
PS3551 worms, DMSO, rep 3 |
| GSM8404227 |
PS3551 worms, DMSO, rep 4 |
| GSM8404228 |
RB754 worms, atRA, rep 1 |
| GSM8404229 |
RB754 worms, atRA, rep 2 |
| GSM8404230 |
RB754 worms, atRA, rep 3 |
| GSM8404231 |
RB754 worms, atRA, rep 4 |
| GSM8404232 |
RB754 worms, DMSO, rep 1 |
| GSM8404233 |
RB754 worms, DMSO, rep 2 |
| GSM8404234 |
RB754 worms, DMSO, rep 3 |
| GSM8404235 |
RB754 worms, DMSO, rep 4 |
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| Relations |
| BioProject |
PRJNA1137311 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE272535_N2_featureCounts.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
| GSE272535_PS3551_featureCounts.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
| GSE272535_RB754_featureCounts.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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