Different developmental trajectories of ovaries in Siberian hamsters raised in long and short day lengths
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus Phodopus sungorus
PROVIDER: GSE50869 | GEO | 2013/09/14
SECONDARY ACCESSION(S): PRJNA219204
REPOSITORIES: GEO
Similar Datasets
Project description:A genome-wide association study was performed on ovaries from Siberian hamsters raised in either long or short photoperiod. Few differences between long and short photoperiod were noted at 3 wk of age, when ovarian histology was identical, whereas many differences in gene expression were noted at 8 wk of age, when ovarian histologies were markedly different. Hamsters were gestated and maintained in 16 or 10 hours of light per day, the latter short photoperiod delays sexual maturity and alters ovarian histology. Differences in gene expression were evaluated by microarray at 3 and 8 wk of age, as were changes between 3 and 8 wk of age in each photoperiod.
2013-09-14 | E-GEOD-50869 | biostudies-arrayexpress
Project description:The mechanism(s) involved in the regulation of the seasonal-appropriate body weight of the Siberian hamster is currently unknown. We have identified photoperiodically regulated genes including VGF in a sub-region of the arcuate nucleus termed the dorsomedial posterior arcuate (dmpARC). Gene expression changes in this nucleus so far account for a significant number of those reported as photoperiodically regulated and are therefore likely to contribute to seasonal physiological responses of the hamsters. The present study was conducted to identify additional genes expressed in the dmpARC regulated by photoperiod that could be involved in regulating the activity of this nucleus with respect to seasonal physiology of the Siberian hamster. Using laser capture microdissection coupled with a microarray analysis and a candidate gene approach, we have identified in the dmpARC several photoperiodically regulated genes that are known to have roles in secretory and intracellular signaling pathways. These include secretogranin III (SgIII) and SgVI (secretory pathway), melanocortin 3 receptor (MC3-R) and serotonin (5-HT) receptors 2A and 7 (signaling pathway), all of which increase in expression in short photoperiod. The spatial relationship between receptor signaling and potential secretory pathways was investigated by dual in situ hybridization, which revealed that 5-HT2A and 5-HT7 receptors are expressed in neurons expressing VGF mRNA and that a sub-population (approximately 40%) of these neurons express MC3-R. These gene expression changes in dmpARC neurons may reflect the functional requirement of these neurons for seasonal physiology responses of the hamster Samples were taken from 10 individual animals, 5 of which had lived under a short day (SD) photoperiod, the other 5 under a long day (LD) photoperiod. Each hybridisation compared a LD sample (labelled with Cy5) with a SD sample (labelled with Cy3).
2010-05-15 | E-GEOD-10278 | biostudies-arrayexpress
Project description:The mechanism(s) involved in the regulation of the seasonal-appropriate body weight of the Siberian hamster is currently unknown. We have identified photoperiodically regulated genes including VGF in a sub-region of the arcuate nucleus termed the dorsomedial posterior arcuate (dmpARC). Gene expression changes in this nucleus so far account for a significant number of those reported as photoperiodically regulated and are therefore likely to contribute to seasonal physiological responses of the hamsters. The present study was conducted to identify additional genes expressed in the dmpARC regulated by photoperiod that could be involved in regulating the activity of this nucleus with respect to seasonal physiology of the Siberian hamster. Using laser capture microdissection coupled with a microarray analysis and a candidate gene approach, we have identified in the dmpARC several photoperiodically regulated genes that are known to have roles in secretory and intracellular signaling pathways. These include secretogranin III (SgIII) and SgVI (secretory pathway), melanocortin 3 receptor (MC3-R) and serotonin (5-HT) receptors 2A and 7 (signaling pathway), all of which increase in expression in short photoperiod. The spatial relationship between receptor signaling and potential secretory pathways was investigated by dual in situ hybridization, which revealed that 5-HT2A and 5-HT7 receptors are expressed in neurons expressing VGF mRNA and that a sub-population (approximately 40%) of these neurons express MC3-R. These gene expression changes in dmpARC neurons may reflect the functional requirement of these neurons for seasonal physiology responses of the hamster
2008-11-29 | GSE10278 | GEO
Project description:Siberian A. lyrata short-read data
| PRJEB67879 | ENA
Project description:Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels, increased blood pressure, short stature and broad skulls that have been attributed to adaptation to the extreme cold climate. We have genotyped 200 individuals from ten indigenous Siberian populations for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. We present a list of cold adaption candidate genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture. 200 blood samples from 200 Siberian individuals that come from ten different indigenous populations were genotypes for 730,525 SNPs across the genome. Eighteen Vietnamese samples were also genotyped and used as reference samples.
2014-03-05 | E-GEOD-55586 | biostudies-arrayexpress
Project description:Following the dispersal out of Africa, where hominins evolved in warm environments for millions of years, our species has colonised different climate zones of the world, including high latitudes and cold environments. The extent to which human habitation in (sub-)Arctic regions has been enabled by cultural buffering, short-term acclimatization and genetic adaptations is not clearly understood. Present day indigenous populations of Siberia show a number of phenotypic features, such as increased basal metabolic rate, low serum lipid levels, increased blood pressure, short stature and broad skulls that have been attributed to adaptation to the extreme cold climate. We have genotyped 200 individuals from ten indigenous Siberian populations for 730,525 SNPs across the genome to identify genes and non-coding regions that have undergone unusually rapid allele frequency and long-range haplotype homozygosity change in the recent past. At least three distinct population clusters could be identified among the Siberians, each of which showed a number of unique signals of selection. We present a list of cold adaption candidate genes that showed significant signals of positive selection with our strongest signals associated with genes involved in energy regulation and metabolism (CPT1A, LRP5, THADA) and vascular smooth muscle contraction (PRKG1). By employing a new method that paints phased chromosome chunks by their ancestry we distinguish local Siberian-specific long-range haplotype signals from those introduced by admixture.
2014-03-05 | GSE55586 | GEO
Project description:Purpose: Photoperiod is known to cause physiological changes in seasonal mammals, including body weight, physical activity, and reproductive status. Because cats are seasonal breeders, we recently tested the effects of day length on resting metabolic rate, voluntary physical activity, and food intake. In that study, resting metabolic rate, physical activity, and food intake to maintain body weight were greater in cats exposed to long days vs. short days. Because photoperiod has also been demonstrated to affect adipose tissue gene expression in several species, including dairy cows, sheep, and Siberian hamsters, the objective of this study was to determine the effects of day length on the adipose transcriptome profile of cats as assessed by RNA-seq. Methods: Ten healthy adult neutered male domestic shorthair cats were used in a randomized crossover design study. During two 12-wk periods, cats were exposed to either short days (8 hr light:16 hr dark) or long days (16 hr light:8 hr dark). Cats were fed a commercial diet to maintain baseline body weight. Subcutaneous adipose biopsies were collected at wk 12 of each period for RNA isolation and Illumina sequencing. Results: A total of 578 million sequences (28.9 million/sample) were generated by Illumina sequencing. Using a raw p value of P<0.005, 170 mRNA transcripts were differentially expressed between short day- and long day-housed cats. Of the 170 transcripts highlighted, 25 annotated transcripts were up-regulated, while 116 annotated transcripts were down-regulated by long days. Another 29 un-annotated transcripts (name and function not known) were also different between groups. In general, adipose tissue of long day-housed cats had greater expression of genes involved with cholesterol trafficking, fatty acid synthesis and immune function, and lower expression of genes involved with cell cycle and growth, cell development and structure, and protein processing, when compared to short day-housed cats.
2014-01-01 | GSE46431 | GEO
Project description:Purpose: Photoperiod is known to cause physiological changes in seasonal mammals, including body weight, physical activity, and reproductive status. Because cats are seasonal breeders, we recently tested the effects of day length on resting metabolic rate, voluntary physical activity, and food intake. In that study, resting metabolic rate, physical activity, and food intake to maintain body weight were greater in cats exposed to long days vs. short days. Because photoperiod has also been demonstrated to affect adipose tissue gene expression in several species, including dairy cows, sheep, and Siberian hamsters, the objective of this study was to determine the effects of day length on the adipose transcriptome profile of cats as assessed by RNA-seq. Methods: Ten healthy adult neutered male domestic shorthair cats were used in a randomized crossover design study. During two 12-wk periods, cats were exposed to either short days (8 hr light:16 hr dark) or long days (16 hr light:8 hr dark). Cats were fed a commercial diet to maintain baseline body weight. Subcutaneous adipose biopsies were collected at wk 12 of each period for RNA isolation and Illumina sequencing. Results: A total of 578 million sequences (28.9 million/sample) were generated by Illumina sequencing. Using a raw p value of P<0.005, 170 mRNA transcripts were differentially expressed between short day- and long day-housed cats. Of the 170 transcripts highlighted, 25 annotated transcripts were up-regulated, while 116 annotated transcripts were down-regulated by long days. Another 29 un-annotated transcripts (name and function not known) were also different between groups. In general, adipose tissue of long day-housed cats had greater expression of genes involved with cholesterol trafficking, fatty acid synthesis and immune function, and lower expression of genes involved with cell cycle and growth, cell development and structure, and protein processing, when compared to short day-housed cats. Subcutaneous adipose tissue mRNA profiles of healthy adult neutered male cats exposed to short days (8 hr light: 16 hr dark) or long days (16 hr light: 8 hr dark) using Illumina sequencing.
2014-01-01 | E-GEOD-46431 | biostudies-arrayexpress
Project description:Ancient Siberian wolf sequencing
| PRJEB7788 | ENA
Project description:Metagenomes from Siberian permafrost Raw sequence reads
| PRJNA601698 | ENA