RIP-chip analysis of the C. elegans PUF protein FBF

The PUF family of RNA binding proteins has a conserved role in maintaining stem cell self-renewal. FBF is a C. elegans PUF that is required to maintain germline stem cells (GSCs). To understand how FBF controls GSCs, we sought to identify is target mRNAs. Briefly, we immunoprecipitated FBF-mRNA complexes from worm extracts and then used microarrays to identify the FBF-associated mRNAs. To focus on germline targets of FBF, we used a FBF-GFP transgene under the control of a germline promoter and we used an anti-GFP antibody to purify FBF-GFP from worm extracts. In parallel, we also processed a strain expressing TUBULIN-GFP in the germline to control for mRNAs that non-specifically co-purify with GFP. We found that FBF associates with >1,000 unique mRNAs and likely controls a broad network of key cellular and developmental regulators.

Expression Data of Reactive Oxygen Species Signalling in C. elegans

We have shown that worms that possess mutations in two electron transport chain subunits live longer due to mtROS signalling. Wild type worms can also live longer by treatment with the pro-oxidant paraquat. Paraquat treatment is not additive to the mutations in the ETC subunits. We aimed to determine the underlying changes in gene expression that were common to both paraquat treatment and the two mutations. We also have shown genetically that the mtROS signal that leads to extended lifespan is dependent on CED-4. We generated double mutants that lack functional CED-4 with the two mutations in the ETC subunits. We have found that a large number of gene expression changes by mtROS signalling are reverted by loss of CED-4.

Expression data from glp-1(e2141) hermaphrodites maintained with or without males for 8 days

Males induce dramatic physiological changes to hermaphrodites, including a significant shortening of lifespan. We have termed this effect as male-induced demise (MID) of hermaphrodites. This experiment was performed to analyse changes in gene expression due to the presence of males. We have shown that Knock down of utx-1 ameliorates the MID. In this experiment we also examine male-induce gene expression that may be altered when knocking down expression of utx-1 via RNAi. We used microarrays to detail the global program of gene expression andidentified distinct classes of up-regulated and down-regulated genes upon the addition of males.

Transcriptomic response of young adult N2, xpa1, and glp1 nematodes 3h after exposure to 50 J/m2 UVC radiation at 25C

We compared the transcriptomic response to UVC radiation in widltype (N2), DNA repair-deficient (xpa-1), and germ cell-deficient (glp-1) young adult nematodes. We were interested in the wildtype response to this stressor, and postulated that the early (3h post-exposure) difference might be different in nucleotide excision repair-deficient (xpa-1) nematodes. We also hypothesized that the response would be different in young adults composed entirely of somatic cells (glp-1 strain at this temperature), compared to germ cell-bearing and gravid young adults (N2 and xpa-1). Finally, we compared constitutive differences in gene expression between the strains.

C. briggsae developmental timecourse

To identify differences in gene expression patterns between C. elegans and C. briggsae we designed whole-genome species-specific microarrays.

C. briggsae developmental timecourse

To identify differences in gene expression patterns between C. elegans and C. briggsae we designed whole-genome species-specific microarrays.

Gene expression profile of C. elegans worms when mekk-3 is knocked down by RNAi

We have discovered a novel gene, mekk-3/idr-1, which when knocked down by RNAi dramatically increases life span. In order to understand how this gene works, we performed microarray analysis to compare the gene expression profiles of control and mekk-3/idr-1 RNAi-grown worms.

C.elegans gene expression study for single, double or triple genetic perturbations of regulators in AMPK, Insulin and TOR pathway

We use genetic manipulations of regulators representing different pathways to examine whether transcriptomes progressively resemble dietary restriction when multiple regulators are perturbed.

Adult aging in C. elegans

We wished to study normal adult aging in C. elegans. We competitively hybridized a series of experimental samples (experimental variable: adult age) against a common reference sample. We use the CF512 fer-15(b26) II; fem-1 (hc17) IV mutant strain, which has defective spermatids which fail to activate into spermatozoa at 25C. Culturing this strain at 25C prevented self-fertilization and therefore eliminated contributions from embryonic transcripts. CF512 animals develop an otherwise-normal germ line; their lifespan and aging are similar to wild-type animals. We axenized eggs and then synchronized animals via L1 arrest. Populations were very tightly synchronized. Animals were cultured at 25C. Samples were extracted and hybridized as described in protocols at http:

Expression data of isp-1(qm150);ctb-1(qm189) mutant, exposed to klf-1 RNAi during development or adulthood

We showed that KLF-1 is needed for longevity of isp-1(qm150);ctb-1(qm189) mutant specifically in adulthood. We aimed to determine the expression changes that occur specifically upon adulthood klf-1 RNAi compared to developmental RNAi that did not affect the lifespan of isp-1(qm150);ctb-1(qm189) mutant.