GEO DataSets

(Submitter supplied) In this work, we examined the effect of the transcription factor ATFS-1 in the long lifespan of the nuo-6 mitochondrial mutant. We also examined the effect of the hypoxia transcription factor hif-1. We sequenced both atfs-1 deletion mutants and atfs-1 gain-of-function point mutants in which the mitochondrial localization sequence of ATFS-1 is disrupted. Note that sequencing batch 2 was previously uploaded as part of GSE93724.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19757

43 Samples

Download data: TXT

(Submitter supplied) Long-lived genetic mutants from different pathways of lifespan extension were used to determine the extent to which there are common downstream mediators of longevity. We have previously obtained RNA-sequencing data from other long-lived mutants including sod-2, clk-1, isp-1, nuo-6 and daf-2. Gene expression will be compared between these nine long-lived mutants.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19757

36 Samples

Download data: CSV

(Submitter supplied) isp-1;sod double mutants have decreased lifespan, increased resistance to oxidative stress and slow physiologic rates. We performed RNA sequencing to compare gene expression between isp-1 mutants and isp-1;sod-3 and isp-1;sod-5 double mutants

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19757

12 Samples

Download data: TXT

(Submitter supplied) Mild deficits in mitochondrial function have been shown to increase lifespan in multiple species including worms, flies and mice. Here, we study three C. elegans mitochondrial mutants (clk-1, isp-1 and nuo-6) to identify overlapping genetic pathways that contribute to their longevity. We find that genes regulated by the FOXO transcription factor DAF-16 are upregulated in all three strains, and that the transcriptional changes present in these worms overlap significantly with the long-lived insulin-IGF1 signaling pathway mutant daf-2. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19757

51 Samples

Download data: TXT

(Submitter supplied) To better understand genome coordination and OXPHOS recovery during mitochondrial dysfunction, we examined ATFS-1, a transcription factor that regulates mitochondria-to nuclear communication during the mitochondrial UPR, via ChIP-sequencing.

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18245

2 Samples

Download data: TXT

(Submitter supplied) ATFS-1 has been shown to regulate transcription of mitochondrial chaperone genes such as mtHsp70/hsp-6 and hsp-60 in response to mitocondrial stress. To identify the entire ATFS-1-mediated response, we compared the transcript profiles from wild-type and atfs-1(tm4525) worms raised in the absence and presence of mitochondrial stress. We used microarrays to identify genes regulated by ATFS-1 during mitochondrial stress

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Dataset:

GDS4570

Platform:

GPL200

12 Samples

Download data: CEL, CHP

Analysis of atfs-1 mutants raised on spg-7(RNAi) which induces mitochondrial stress (MS). ATFS-1 (activating transcription factor associated with stress-1) senses MS and communicates with the nucleus during the mitochondrial unfolded protein response. Results provide insight into the MS response.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array, count, 2 genotype/variation, 2 protocol sets

Platform:

GPL200

Series:

GSE38196

12 Samples

Download data: CEL, CHP

(Submitter supplied) To adapt mitochondrial function to the ever-changing intra- and extra-cellular environment, multiple mitochondrial stress response (MSR) pathways, including the mitochondrial unfolded protein response (UPRmt), have evolved. However, how the mitochondrial stress signal is sensed and relayed to UPRmt transcription factors, such as ATFS-1 in Caenorhabditis elegans, remains largely unknown. Here, we show that a panel of vacuolar H+-ATPase (v-ATPase) subunits and the target of rapamycin complex 1 (TORC1) activity are essential for the cytosolic relay of mitochondrial stress to ATFS-1, and for the induction of the UPRmt. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25145

36 Samples

Download data: XLS

(Submitter supplied) Comparison of gene change in the atfs-1 (null) to WT. Comparison of gene change in the atfs-1 (et18) to WT.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

12 Samples

Download data: TXT

(Submitter supplied) Dietary restriction (DR) and loss of the genes rsks-1 and daf-2 increase longevity in C. elegans. Polysome profiling allows actively translated mRNA bound by multiple ribosomes to be isolated and compared to the total mRNA present. In this project, we differentiate transcriptional and translational changes in gene expression in C. elegans by combining polysome profiling and mRNA-sequencing. By comparing gene abundance between the two RNA pools, genes with altered translational regulation under DR and in the mutant can be identified.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

24 Samples

Download data: TXT

(Submitter supplied) Analysis of genes differentially expressed between daf-2(e1368) and daf-2(e1368);pmk-1(km25) and between daf-2(e1368) and daf-2(e1368);daf-16(mgDf47). These studies identified genes upregulated by wild-type PMK-1 and wild-type DAF-16. Keywords: genetic modification

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Dataset:

GDS3253

Platform:

GPL200

9 Samples

Download data: CEL

(Submitter supplied) Analysis of differential gene expression in C. elegans adults exposed to three different bacteria: E. coli strain OP50, wild-type P. aeruginosa PA14 and gacA mutant PA14. Samples were analyzed at 4 hours and 8 hours after exposure to the different bacteria. These studies identified C. elegans genes induced by pathogen infection. Keywords: Time course, response to pathogen infection

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Dataset:

GDS3252

Platform:

GPL200

18 Samples

Download data: CEL

Analysis of daf-2(e1368) loss-of-function mutant and daf-2(e1368);pmk-1(km25) and daf-2(e1368);daf-16(mgDf47) double mutants. PMK-1 and DAF-16 confer enhanced pathogen resistance on daf-2 mutants relative to wild-type. Results suggest DAF-16 and PMK-1 upregulate distinct genes to promote immunity.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array, count, 3 genotype/variation sets

Platform:

GPL200

Series:

GSE5801

9 Samples

Download data: CEL

Analysis of strain fer-15(b26);fem-1(hc17) young adults exposed for up to 8 hrs to pathogenic Pseudomonas aeruginosa strain PA14, less pathogenic PA14 mutant gacA, and E. coli strain OP50 (normal food source). Results provide insight into the molecular basis of the response to a bacterial pathogen.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array, count, 3 infection, 2 time sets

Platform:

GPL200

Series:

GSE5793

18 Samples

Download data: CEL

(Submitter supplied) Aging and the age-associated decline of the proteome is determined in part through neuronal control of evolutionarily conserved transcriptional effectors, which safeguard homeostasis under fluctuating metabolic and stress conditions by regulating an expansive proteostatic network. We have discovered the Caenorhabditis elegans homeodomain-interacting protein kinase (HPK-1) acts as a key transcriptional effector to preserve neuronal integrity, function, and proteostasis during aging. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18245

6 Samples

Download data: TXT

(Submitter supplied) Across eukaryotic species, mild mitochondrial stress can have beneficial effects on the lifespan of organisms. Mitochondrial dysfunction activates an unfolded protein response (UPRmt), a stress signaling mechanism designed to ensure mitochondrial homeostasis. Perturbation of mitochondria during larval development in C. elegans not only delays aging but also maintains UPRmt signaling, suggesting an epigenetic mechanism that modulates both longevity and mitochondrial proteostasis throughout life. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18245

15 Samples

Download data: TXT

(Submitter supplied) Mitochondrial Quality Control (MQC) balances organelle adaptation and elimination, and mechanistic crosstalk between the underlying molecular processes impacts subsequent stress outcomes. FUN14 Domain Containing 1 (FUNDC1) is a mammalian mitophagy receptor that responds to hypoxia-reoxygenation (HR) stress. Here, we provide evidence that FNDC-1 is the C. elegans ortholog of FUNDC1, and that its loss protects against injury in a worm model of HR. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19757

15 Samples

Download data: TXT

(Submitter supplied) Oxidative stress may play a role in normal aging. SKN-1 is a transcription factor necessary for intestine development in Caenorhabditis elegans, which also regulates the response to oxidative stress post-embryonically. Using DNA microarrays, we found that oxidative stress induces the antioxidant response, the heat shock response, and detoxification genes, while the expression of genes involved in homeostasis, development, and reproduction were decreased. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

11 Samples

Download data: CEL

(Submitter supplied) A forward genetic screen identified a mutation in the previously uncharacterized gene F01D4.5--homologous with human TCF20 and RAI1--that suppresses the adverse phenotypes observed in m-tyrosine-treated tyrosine aminotransferase mutant C. elegans. To gain insights into the function of F01D4.5. RNA was isolated from N2 and F01D4.5(baf20) mutants and used for whole transcriptome profiling by RNA sequencing. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24892

10 Samples

Download data: TXT

(Submitter supplied) We previously identified a number of genes which were differentially expressed during mitochondrial stress in an ATFS-1-dependent manner using an atfs-1 loss-of-function mutant allele . To complement the findings from our previous microarray, we compared the transcript profiles from wild-type and atfs-1(et18) gain-of-function worms (which have constitutively active ATFS-1) in the absence of mitochondrial stress. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

6 Samples

Download data: CEL, CHP