Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of muscle from wild type and fer-1 mutant C. elegans

ABSTRACT: In vertebrate muscle, loss of Dysferlin results in the activation of compensatory muscle gene expression, even at pre-pathological stages. We hypothesized that if C. elegans fer-1 is also expressed in muscle, then fer-1 mutant worms might also exhibit compensatory muscle gene expression. To test this hypothesis, we used Affymetrix microarrays to profile gene expression from synchronized wild type and fer-1 mutant adults. To improve the specificity of this approach, we profiled two well characterized loss-of-function fer-1 mutants (hc1ts and hc24ts) and considered genes that changed similarly in both mutants as fer-1-regulated transcripts. Experiment Overall Design: For each genotype, six individual replicates were performed and were hybridized to Affymetrix C. elegans Genechips using the manufacturerâs recommended protocols. The best four preparations (as determined by the overall Pearson Correlation within a genotype) were used for RNA labeling and hybridization.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Predrag Krajacic

PROVIDER: E-GEOD-16753 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

C. elegans fer-1 mutant gene expression profile

Project description:In vertebrate muscle, loss of Dysferlin results in the activation of compensatory muscle gene expression, even at pre-pathological stages. We hypothesized that if C. elegans fer-1 is also expressed in muscle, then fer-1 mutant worms might also exhibit compensatory muscle gene expression. To test this hypothesis, we used Affymetrix microarrays to profile gene expression from synchronized wild type and fer-1 mutant adults. To improve the specificity of this approach, we profiled two well characterized loss-of-function fer-1 mutants (hc1ts and hc24ts) and considered genes that changed similarly in both mutants as fer-1-regulated transcripts.

2009-06-25 | GSE16753 | GEO

Transcription profiling of long-lived C.elegans daf-2 pathway mutants with wild type/short-lived mutants

Project description:Comparison of long-lived daf-2 pathway mutants with wild type/short-lived mutants. A: age-1 fer-15; fem-1 vs. fer-15; fem-1. B: age-1 fer-15; fem-1 vs. fer-15; fem-1. C: fer-15; daf-2(mu150); fem-1 vs. fer-15; fem-1. D: fer-15; daf-2(mu150); fem-1 vs. fer-15; fem-1. E: daf-16::gfp in daf-16(mu86);daf-2(e1370) vs. daf-16(mu86);daf-2(e1370). F: daf-2(e1368); fer-15; fem-1 vs. fer-15; fem-1. G: fer-15; daf-2(mu150); fem-1 vs. fer-15; fem-1. H: age-1 fer-15; fem-1 vs. fer-15; fem-1. I: fer-15; daf-2(mu150); fem-1 vs. fer-15; fem-1. J: daf-16::gfp in daf-2(e1370); daf-16(mu86) vs. daf-2(e1370); daf-16(mu86). K: daf-2(mu150) vs. wild type. L: daf-2(e1370) vs. daf-2(e1370); daf-16(mu86). M: daf-2(e1370) vs. daf-2(e1370); daf-16(mu86). N: daf-2(e1370) vs. daf-2(e1370); daf-16(mu86).

2003-07-17 | E-MEXP-7 | biostudies-arrayexpress

Transcription profiling of C. elegans wildtype and gas-1 mitochondrial mutants

Project description:Utilizing C. elegans as a model of mitochondrial dysfunction provides insight into cellular adaptations which occur as a consequence of genetic alterations causative of human disease. We characterized genome-wide expression profiles of hypomorhpic C. elegans mutants in nuclear-encoded subunits of respiratory chain complexes I, II and III. Our goal was to detect concordant changes among clusters of genes that comprise defined metabolic pathways utilizing gene set enrichment analysis. Experiment Overall Design: 5 biological replicates of wildtype and electron transport chain (ETC) mutant C. elegans were used as sources of total RNA, each for hybridization to a single Affymetrix whole-genome microarray. Comparison of the data was intended to reveal metabolic pathways downstream of the mutation.

2008-04-07 | E-GEOD-9896 | biostudies-arrayexpress

Transcription profiling of C. elegans complex RNAi mutant vs wildtype

Project description:This SuperSeries is composed of the following subset Series:; GSE9896: Expression data from wildtype and gas-1 mitochondrial mutant C. elegans; GSE9897: Expression data from 2 wildtype and 8 C. elegans ETC mutants Experiment Overall Design: Refer to individual Series

2008-04-08 | E-GEOD-9967 | biostudies-arrayexpress

Transcription profiling of C. elegans wild type and 5 osmotic stress resistant mutants exposed to hyper/isotonic environments

Project description:Adaptation of C. elegans to hypertonic environments involves the accumulation of the organic osmolyte glycerol via transcriptional upregulation of the glycerol biosynthestic enzyme gpdh-1. A number of mutants, termed osmotic stress resistant (osr) mutants, have been identified. osr mutants cause constitutive upregulation of gpdh-1 and confer extreme resistance to hypertonicity. We tested the hypothesis that osr mutants broadly activate a gene expression program normally activated by osmotic stress in wild type animals using Affymterix microarray analysis of the hypertonic stress response in wild type animals and of constituitive gene expression changes in five osr mutants. Experiment Overall Design: Young adult C. elegans were exposed to hypertonic growth plates for varying times prior to RNA extraction and hybridization on Affymetrix microarrays. Since we wished to separate direct response from secondary responses to osmotic stress, we collected worms following short term exposures to hypertonic conditions (15 minutes and 1 hour) and after long term exposure to hypertonic conditions (6 hours or a full generation of growth under hypertonic conditions). We also collected young adults from the osr mutants osm-7, osm-8, osm-11, dpy-9, and dpy-10 for microarray analysis. These mutants were grown under isotonic conditions to determine whether that constitutively activate genes normally regulated by hypertonic stress in wild type animals.

2009-12-14 | E-GEOD-19310 | biostudies-arrayexpress

Unusual DNA packaging characteristics in endo-reduplicated C. elegans oocytes defined by in vivo accessibility to an endogenous nuclease activity

Project description:We describe DNA-surface interactions in activated C. elegans oocytes that are revealed through the activity of an endogenous nuclease. Our analysis began with an unexpected observation that a majority (>50%) of DNA from C. elegans fer-1 oocytes can be recovered in fragments of ~500 base pairs or shorter, cleaved at regular intervals (10-11nt) along the DNA helix. In some areas of the genome, cleavage patterns in the endoreduplicated oocytes appear consistent from cell-to-cell, indicating coherent rotational positioning of the DNA in chromatin. Particularly striking in this analysis are arrays of sensitive sites with a periodicity of ~10bp that persist for several hundred base pairs of genomic DNA, longer than a single nucleosome core. Genomic regions with a strong bias toward a 10-nt periodic occurrence of A(n)/T(n) (so-called PATC regions) appear to exhibit a high degree of rotational constraint in endo-cleavage phasing, with a strong tendency for the periodic A(n)/T(n) sites to remain on the face of the helix protected from nuclease digestion. Overall, the present analysis provides evidence for an unusual structure in C. elegans oocytes in which genomic DNA and associated protein structures are coherently linked. Examine endocleavage pattern in C. elegans fer-1 oocyte chromatin

2013-07-01 | E-GEOD-46499 | biostudies-arrayexpress

RNAi knock down of daf-2, daf-3, daf-16 in C. elegans over 0-48 hours

Project description:Comparison of sterile worms grown on Control Vector, daf-2 RNAi, and daf-2 + daf-16 RNAi. Synchronized fer-15(b26); fem-1(hc17) animals were grown on RNAi bacteria at 25ºC, induced with IPTG on Day 1 of adulthood, and collected from 0-48 hours (10 time points) and 0-196 hours (10 time points); RNAi bacteria was supplemented as necessary for later time points. Worms were floated off lawns with M9 buffer, centrifuged, and washed again in M9. The pelleted worms were dissolved in Trizol (Gibco) and frozen in liquid nitrogen.Time courses were compared with mixed references (collected from 1/2 of each of the time course samples)

2003-07-17 | E-MEXP-8 | biostudies-arrayexpress

RNAi knock down of daf-16 in C. elegans over 0-192 hours

2003-07-17 | E-MEXP-9 | biostudies-arrayexpress

Transcription profiling of C. elegans exposed to the fungal pathogen Drechmeria coniospora for 24 hours

Project description:Response of C. elegans to Drechmeria coniospora infection at 24 hours.

2007-07-03 | E-MEXP-768 | biostudies-arrayexpress

Transcription profiling of C. elegans exposed to the fungal pathogen Drechmeria coniospora for 12 hours

Project description:Response of C. elegans to infection by Drechmeria coniospora at 12 hours.

2007-07-03 | E-MEXP-767 | biostudies-arrayexpress