Ontology highlight
ABSTRACT:
PROVIDER: PRJNA604787 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11016521_1.fastq.gz | Fastqsanger.gz | |||
| SRR11016521_2.fastq.gz | Fastqsanger.gz | |||
| SRR11016522_1.fastq.gz | Fastqsanger.gz | |||
| SRR11016522_2.fastq.gz | Fastqsanger.gz | |||
| SRR11016523_1.fastq.gz | Fastqsanger.gz |
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Project description:Southern California (USA) populations of the intertidal marine snail Chlorostoma (formerly Tegula) funebralis are generally exposed to higher air and water temperatures than northern California populations. Previous studies have shown that southern populations are more tolerant of heat stress than northern populations. To assess the potential role of gene regulation in these regional differences, we examined transcriptome responses to thermal stress in two southern and two northern populations of C. funebralis. Snails from the four populations were acclimated to a common lab environment, exposed to a heat stress representative of natural low tide conditions, and then analyzed using RNA-Seq to characterize changes in gene expression associated with stress and differences in expression across geographic regions. Changes in expression following stress were dominated by genes involved in apoptosis, the inflammatory response, response to mis and unfolded proteins, and ubiquitination of proteins. Heat shock proteins (Hsps) were up-regulated in both northern and southern populations. However, while the magnitude of the response was significantly greater in northern populations for the majority of Hsp70s, the southern populations showed a greater up-regulation for roughly half of the Hsp40s, which are co-chaperones for Hsp70s. Differential expression analysis of the control versus treatment genes in the northern and southern populations respectively revealed that 56 genes, many involved in the inflammation and immune response, responded to heat stress only in the northern populations. Moreover, several of the molecular chaperones and antioxidant genes that were not differentially expressed in the southern populations instead showed higher constitutive expression under control conditions compared to the northern populations. The expression levels of some of these constitutive genes such as superoxide dismutase were also found to positively correlate with survival following heat stress. This suggests that expression of these genes has evolved a degree of M-bM-^@M-^\frontloadingM-bM-^@M-^] that may contribute to the higher thermal tolerance of southern populations. mRNA profiles of northern and southern California heat-stressed and control C. funebralis were generated by 100bp paired end sequencing, in duplicate, using Illumina HiSeq2000.
2014-08-20 | E-GEOD-57142 | biostudies-arrayexpress
Project description:Southern California (USA) populations of the intertidal marine snail Chlorostoma (formerly Tegula) funebralis are generally exposed to higher air and water temperatures than northern California populations. Previous studies have shown that southern populations are more tolerant of heat stress than northern populations. To assess the potential role of gene regulation in these regional differences, we examined transcriptome responses to thermal stress in two southern and two northern populations of C. funebralis. Snails from the four populations were acclimated to a common lab environment, exposed to a heat stress representative of natural low tide conditions, and then analyzed using RNA-Seq to characterize changes in gene expression associated with stress and differences in expression across geographic regions. Changes in expression following stress were dominated by genes involved in apoptosis, the inflammatory response, response to mis and unfolded proteins, and ubiquitination of proteins. Heat shock proteins (Hsps) were up-regulated in both northern and southern populations. However, while the magnitude of the response was significantly greater in northern populations for the majority of Hsp70s, the southern populations showed a greater up-regulation for roughly half of the Hsp40s, which are co-chaperones for Hsp70s. Differential expression analysis of the control versus treatment genes in the northern and southern populations respectively revealed that 56 genes, many involved in the inflammation and immune response, responded to heat stress only in the northern populations. Moreover, several of the molecular chaperones and antioxidant genes that were not differentially expressed in the southern populations instead showed higher constitutive expression under control conditions compared to the northern populations. The expression levels of some of these constitutive genes such as superoxide dismutase were also found to positively correlate with survival following heat stress. This suggests that expression of these genes has evolved a degree of “frontloading” that may contribute to the higher thermal tolerance of southern populations.
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Project description:We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS) formed by crossing four inbred strains (HS4) and a heterogeneous stock (HS-CC) formed from the inbred strain founders of the Collaborative Cross (CC). All three selections were successful, with large differences in haloperidol response emerging within three generations. Genome-wide analysis between the selected lines revealed post-selection loss of allelic diversity concurrent with significant genetic differences. In spite of large phenotypic differences, absolute gene-expression changes were modest and not concordant across selections. However, gene coexpression patterns changed significantly, as revealed by the weighted gene co-expression network analysis. In particular, we detected three modules (de novo subnetworks) that (a) were functionally enriched for neurobehavioral traits and (b) showed independently detectable changes in network connectivity across selections. By inferring strain contributions from the parental lines, we are able to identify significant differences in allelic content between the selected lines concurrent with large changes in transcript connectivity. Importantly, this observation implies that genetic polymorphisms can affect transcript and module connectivity without large changes in absolute expression levels. We conclude that, in this case, selective breeding acts at the subnetwork level, with the same modules but not the same transcripts affected across the three selections. Equal numbers of males and females (~200 total) from the founder populations (F2, HS4 and HS-CC) were phenotyped for haloperidol response using a two-step process that resulted in assigning animals to one of four groups; “1” was the least responsive, and “4” was the most responsive. Breeding pairs were selected from the most extreme response groups. The selection and breeding were continued for two additional generations; in the third generation, parents were bred for three rounds to produce progeny for gene expression. For each genetic background the submitted samples are labeled as either High or Low based on their response to haloperidol.
2012-05-05 | E-GEOD-37755 | biostudies-arrayexpress
Project description:For the AcceSssIble assay, nuclei preparation and M.SssI methyltransferase (New England BioLabs) treatment were performed. The subsequent Infinium DNA methylation assay was performed at the University of Southern California Molecular Genomics Core Facility according to the manufacturer’s specifications (Illumina).
2018-06-26 | GSE105066 | GEO
Project description:Global warming is causing plastic and evolutionary changes in the phenotypes of ectotherms. Yet, we have limited knowledge on how the interplay between plasticity and evolution shapes thermal responses and underlying gene expression patterns. We assessed thermal reaction norm patterns across the transcriptome and identified associated molecular pathways in northern and southern populations of the damselfly Ischnura elegans. Larvae were reared in a common garden experiment at the mean summer water temperatures experienced at the northern (20 °C) and southern (24 °C) latitudes. This allowed a space-for-time substitution where the current gene expression levels at 24 °C in southern larvae are a proxy for the expected responses of northern larvae under gradual thermal evolution to the predicted 4 °C warming. Most differentially expressed genes showed fixed differences across temperatures between latitudes, suggesting that thermal genetic adaptation will mainly evolve through changes in constitutive gene expression. Northern populations also frequently showed plastic responses in gene expression to mild warming, while southern populations were much less responsive to temperature. Thermal responsive genes in northern populations showed to a large extent a pattern of genetic compensation, i.e. gene expression that was induced at 24 °C in northern populations remained at a lower constant level in southern populations, and were associated with metabolic and translation pathways. There was instead little evidence for genetic assimilation of an initial plastic response to mild warming. Our data therefore suggest that genetic compensation rather than genetic assimilation may drive the evolution of plasticity in response to mild warming in this damselfly species.
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Project description:We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS) formed by crossing four inbred strains (HS4) and a heterogeneous stock (HS-CC) formed from the inbred strain founders of the Collaborative Cross (CC). All three selections were successful, with large differences in haloperidol response emerging within three generations. Genome-wide analysis between the selected lines revealed post-selection loss of allelic diversity concurrent with significant genetic differences. In spite of large phenotypic differences, absolute gene-expression changes were modest and not concordant across selections. However, gene coexpression patterns changed significantly, as revealed by the weighted gene co-expression network analysis. In particular, we detected three modules (de novo subnetworks) that (a) were functionally enriched for neurobehavioral traits and (b) showed independently detectable changes in network connectivity across selections. By inferring strain contributions from the parental lines, we are able to identify significant differences in allelic content between the selected lines concurrent with large changes in transcript connectivity. Importantly, this observation implies that genetic polymorphisms can affect transcript and module connectivity without large changes in absolute expression levels. We conclude that, in this case, selective breeding acts at the subnetwork level, with the same modules but not the same transcripts affected across the three selections.
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