Transcription profiling of Snell dwarf and wild type mouse liver RNA levels in response to 3-NPA (3-nitropropionic acid) sampled at multiple time points
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: John Papaconstantinou
PROVIDER: E-GEOD-1381 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Comparison of Snell Dwarf and Wild Type mouse liver RNA levels in response to 3-NPA (3-nitropropionic acid). Keywords: time-course
2004-06-07 | GSE1381 | GEO
Project description:To compare and contrast genetic signatures from livers of young and aged Snell dwarf mice with their wild type controls. SUBMITTER_CITATION: W. H. Boylston, James H. DeFord, John Papaconstantinou (2006) Identification of longevity-associated genes in long-lived Snell and Ames dwarf mice Age 28:125-144 Experiment Overall Design: 25 micrograms of liver RNA was isolated from each of 6 aged (3 dwarf, 3 wild type) and 8 young (4 dwarf, 4 wild type) mice for use in hybridization of Affymetrix gene chips according to Affymetrix protocols.
2007-12-01 | E-GEOD-3129 | biostudies-arrayexpress
Project description:To compare and contrast genetic signatures from livers of young and aged Snell dwarf mice with their wild type controls. Keywords: Aging
2005-08-16 | GSE3129 | GEO
Project description:To compare and contrast genetic signatures from livers of young and aged Ames dwarf mice with their wild type controls. SUBMITTER_CITATION: W. H. Boylston, James H. DeFord, John Papaconstantinou (2006) Identification of longevity-associated genes in long-lived Snell and Ames dwarf mice Age 28:125-144 Experiment Overall Design: 25 micrograms of liver RNA was isolated from young (5 dwarfs, 5 wildtype), middle aged (5 dwarfs, 5 wild type) and aged (5 dwarf, 6 wild type) mice for use in hybridization of Affymetrix gene chips according to Affymetrix protocols.
2008-06-12 | E-GEOD-3150 | biostudies-arrayexpress
Project description:Despite the progress achieved in elucidating the ecological mechanisms of adaptive radiation, there has been little focus on documenting the extent of adaptive differentiation in physiological functions during this process. Moreover, a thorough understanding of the genomic basis underlying phenotypic adaptive divergence is still in its infancy. One important evolutionary process for which causal genetic mechanisms are largely unknown pertains to life-history trade-offs. We analysed patterns of gene transcription in liver tissue of sympatric dwarf and normal whitefish from two natural lakes, as well as from populations reared in controlled environments, using a 16 006-gene cDNA microarray in order to: (i) document the extent of physiological adaptive divergence between sympatric dwarf and normal species pairs, and (ii) explore the molecular mechanisms of differential life history trade-offs between growth and survival potentially involved in their adaptive divergence. In the two natural lakes, 6.45% of significantly transcribed genes showed regulation either in parallel fashion (2.39%) or in different directions (4.06%). Among genes showing parallelism in regulation patterns, we observed a higher proportion of over-expressed genes in dwarf relative to normal whitefish (70.6%). Patterns observed in controlled conditions were also generally congruent with those observed in natural populations. Dwarf whitefish consistently showed significant over-expression of genes potentially associated with survival through enhanced activity (energy metabolism, iron homeostasis, lipid metabolism, detoxification), whereas more genes associated with growth (protein synthesis, cell cycle, cell growth) were generally down-regulated in dwarf relative to normal whitefish. Overall, parallelism in patterns of gene transcription, as well as patterns of interindividual variation across controlled and natural environments, provide strong indirect evidence for the role of selection in the evolution of differential regulation of genes involving a vast array of potentially adaptive physiological processes between dwarf and normal whitefish. Our results also provide a first mechanistic, genomic basis for the observed trade-off in life-history traits distinguishing dwarf and normal whitefish species pairs, wherein enhanced survival via more active swimming, necessary for increased foraging and predator avoidance, engages energetic costs that translate into slower growth rate and reduced fecundity in dwarf relative to normal whitefish.
2010-03-31 | GSE21130 | GEO
Project description:Rice gall dwarf virus (RGDV) is the causal agent of rice gall dwarf disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RGDV infection.
2012-12-01 | GSE34264 | GEO
Project description:Rice black streak dwarf virus (RBSDV) is the causal agent of rice black streak dwarf disease which causes severe loss of rice yield in Asia countries. In this study, we have analyzed the relationship between symptom and host gene responses by RBSDV infection.
2012-12-01 | GSE34263 | GEO
Project description:Kinase activity of cGMP-dependant, type II, protein kinase (PRKG2) is required for the proliferative to hypertrophic growth transition of growth plate chondrocytes during endochondral ossification. Loss of PRKG2 function in rodent and bovine models results in dwarfism. We compared growth plate cartilage gene expression profiles of PRKG2R678X/R678X, dwarf and PRKG2R678X/+, unaffected Angus cattle using microarray technology to discover pathways regulated by PRKG2. Calves used in this analysis were produced by the mating between a dwarf carrier sire and two dams- a mother (carrier) and daughter (dwarf) pair. Each dam produced three calves by embryo transfer, which were born in two calving groups. Growth plate cartilage was harvested from the tibia of each animal at approximately 215 days of age. Total RNA was extracted by a modified Trizol protocol. The bovine cDNA microarray (GEO Accession: GPL8813) was used for this analysis. Samples were labeled with Cy3 or Cy5 and hybridized by dye swapping the dwarf (4 dwarf animals- 2 per dam/calving group) and unaffected individuals (2 unaffected animals- 1 per dam/ calving group) such that each dwarf was compared to the unaffected full-sib produced in the same calving group. Each cDNA array was analyzed at three different PMT levels (PMT70,80 and 90), resulting in 12 total image files for statistical analysis.
2011-08-25 | GSE31627 | GEO
Project description:Kinase activity of cGMP-dependant, type II, protein kinase (PRKG2) is required for the proliferative to hypertrophic growth transition of growth plate chondrocytes during endochondral ossification. Loss of PRKG2 function in rodent and bovine models results in dwarfism. We compared growth plate cartilage gene expression profiles of PRKG2R678X/R678X, dwarf and PRKG2R678X/+, unaffected Angus cattle using microarray technology to discover pathways regulated by PRKG2. Calves used in this analysis were produced by the mating between a dwarf carrier sire and two dams- a mother (carrier) and daughter (dwarf) pair. Each dam produced three calves by embryo transfer, which were born in two calving groups. Growth plate cartilage was harvested from the tibia of each animal at approximately 215 days of age. Total RNA was extracted by a modified Trizol protocol. The bovine cDNA microarray (GEO Accession: GPL8813) was used for this analysis. Samples were labeled with Cy3 or Cy5 and hybridized by dye swapping the dwarf (4 dwarf animals- 2 per dam/calving group) and unaffected individuals (2 unaffected animals- 1 per dam/ calving group) such that each dwarf was compared to the unaffected full-sib produced in the same calving group. Each cDNA array was analyzed at three different PMT levels (PMT70,80 and 90), resulting in 12 total image files for statistical analysis. Dwarf PRKG2 R678X homozygous cattle were compared to unaffected, age matched samples. Samples were labeled with Cy3 or Cy5 and hybridized by dye swapping the dwarf (4 dwarf animals- 2 per dam/calving group) and unaffected individuals (2 unaffected animals- 1 per dam/ calving group) such that each dwarf was compared to the unaffected full-sib produced in the same calving group (i.e. unaffected samples had 2 technical replicates). Each cDNA array was analyzed at three different PMT levels (PMT70,80 and 90), resulting in 12 total image files for statistical analysis.
2011-08-24 | E-GEOD-31627 | biostudies-arrayexpress