RNA-seq of cold stressed C. elegans
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE337660 | GEO | 2026/07/16
REPOSITORIES: GEO
Similar Datasets
Project description:Cold stressed Azolla and anthocyanins
| PRJEB60373 | ENA
Project description:In this study, we subjected wild type worms and worms deficient in ETS-4, ETS-4 and DAF16, ETS-4 and PQM-1, to cold treatment and analyzed their transcriptional profiles by RNAseq.
2019-05-29 | GSE131870 | GEO
Project description:Low temperature is a major abiotic stress that impedes plant growth and development. Brassica juncea is an economically important oil seed crop and is sensitive to freezing stress during pod filling subsequently leading to abortion of seeds. To understand the cold stress mediated global perturbations in gene expression, whole transcriptome of B. juncea siliques that were exposed to sub-optimal temperature was sequenced. Manually self-pollinated siliques at different stages of development were subjected to either short (6 h) or long (12 h) durations of chilling stress followed by construction of RNA-seq libraries and deep sequencing using Illumina’s NGS platform. De-novo assembly of B. juncea transcriptome resulted in 133641 transcripts, whose combined length was 117 Mb and N50 value was 1428 bp. We identified 13342 differentially regulated transcripts by pair-wise comparison of 18 transcriptome libraries. Hierarchical clustering along with Spearman correlation analysis identified that the differentially expressed genes segregated in two major clusters representing early (5-15 DAP) and late stages (20-30 DAP) of silique development. Further analysis led to the discovery of sub-clusters having similar patterns of gene expression. Two of the sub-clusters (one each from the early and late stages) comprised of genes that were inducible by both the durations of cold stress. Comparison of transcripts from these clusters led to identification of 283 transcripts that were commonly induced by cold stress, and were referred to as ‘core cold-inducible’ transcripts. Additionally, we found that 689 and 100 transcripts were specifically up regulated by cold stress in early and late stages, respectively. We further explored the expression patterns of gene families encoding for transcription factors (TFs), transcription regulators (TRs) and kinases, and found that cold stress induced protein kinases only during early silique development. We validated the digital gene expression profiles of selected transcripts by qPCR and found a high degree of concordance between the two analyses. To our knowledge this is the first report of transcriptome sequencing of cold-stressed B. juncea siliques. The data generated in this study would be a valuable resource for not only understanding the cold stress signaling pathway but also for introducing cold hardiness in B. juncea.
2016-05-21 | GSE73201 | GEO
Project description:Animal models are important tools in scientific research, whereas the animals used are usually single-sex instead of mixed-sex in the experimental design. To better understand the effect of sex difference, we compared several phenotypes between male and female C57BL/6 mice, including behavioral tests, plasma corticosterone levels, adult neurogenesis, and RNA-seq. The experiments were performed under non-stressed and chronic-stressed conditions, respectively. Overall, our results showed several differences between male and female mice in sensorimotor performance while little difference was found in anxiety, depression, learning, and memory. We did not observe a significant difference in adult neurogenesis. There was a sex difference in plasma corticosterone levels under chronic stress conditions, either in 30 min after the restraint stress or after 60min of the recovery. Yet, the corticosterone levels were equivalent between the sexes under non-stressed conditions at any time point. Furthermore, the results of RNA-seq identified the differential expression genes between male and female mice under non-stressed or chronic-stressed conditions.
2022-08-22 | GSE211276 | GEO
Project description:How animals rewire cellular programs to survive cold is a fascinating problem with potential biomedical implications, ranging from emergency medicine to space travel. Studying a hibernation-like response in the free-living nematode Caenorhabditis elegans, we uncovered a regulatory axis that enhances the natural resistance of nematodes to severe cold. This axis involves conserved transcription factors, DAF-16/FoxO and PQM-1, which jointly promote cold survival by upregulating FTN-1, a protein related to mammalian ferritin heavy chain (FTH1). Moreover, we show that inducing expression of FTH1 also promotes cold survival of mammalian neurons, a cell type particularly sensitive to deterioration in hypothermia. Our findings in both animals and cells suggest that FTN-1/FTH1 facilitates cold survival by detoxifying ROS-generating iron species. We finally show that mimicking the effects of FTN-1/FTH1 with drugs protects neurons from cold-induced degeneration, opening a potential avenue to improved treatments of hypothermia.
2022-10-14 | PXD034794 | Pride
Project description:12plex_vitis_2012_04 - cold stress - In temperate species, low temperatures adversely affect plant growth and development, constraining spatial expansion and productivity. Cold can trigger adaptive process or lead to alterations in physiological traits when stress intensity exceeds a certain threshold. Grapevine flower development and fruit set are influenced by cold nights in the vineyard. The correct formation of sexual organs and the success of reproduction are dependent upon sugar supply which can be affected by low temperatures. Many pathways of carbon metabolism may be affected by low temperatures however limited information is available about fluctuations in carbon metabolism in inflorescences. - Experiments were performed on inflorescence of Vitis vinifera L. cv. Pinot noir fruiting cuttings. First, inflorescences at female meiosis were collected the day of the experiment, then cuttings with the inflorescence were placed at 0°C for a 8 h night. Control plants were maintained in a growth chamber for 8 h at 19°C. Inflorescences were collected after 1 h and 8 h of cold. Additional time point was performed 2 h after the end of the cold night by placing the inflorescence at 25°C after the end of the cold night. Control plants were also collected.
2016-10-01 | GSE87296 | GEO
Project description:Stress leads to important adaptive physiological responses including release of catecholamines from the adrenal medulla. Repeated or prolonged stress increases the propensity for many disorders including cardiovascular disease and neuropsychiatric disorders. The susceptibility to stress is determined by a number of factors including prior experience with stress. It has been found that while there is adaptation to prolonged cold stress; it leads to sensitization when cold stressed animals are exposed to a different (novel) stressor. Our study aims to determine the mechanism of this adaptation and sensitization.,We will determine the gene expression patterns in rat adrenal medulla in response to several times of cold stress. We will also determine the changes in gene expression with single immobilization stress in adrenal medulla of rat with and without preexposure to cold stress to investigate the mechanism of sensitization in cold adapted animals. ,We hypothesize that during the course of cold stress there are alterations in gene expression of several neurotransmitter related genes and transcription factors. In cold adapted animals, there is increased susceptibility to stress due to sustained changes in expression of several transcription factors, such as FRA-2 which lead to an exaggerated response to the novel stressor. ,Rats were exposed to cold stress (4oC) for 1, 7 or 28 days. A parallel group was kept at room temperature (unstressed). Unstressed or rats pre-exposed to 28 days cold were immobilized for 2 hrs and killed by decapitation. The adrenal medullae, separately from right and left side, have been dissected and individually frozen at -70oC. Our recent immunoblots with the tissue from one side revealed that there is increase in tyrosine hydroxylase and c-fos with the short term cold stress and in dopamine beta hydroxylase and Fra-2 even with the prolonged cold stress. The response of several transcription factors to immobilization stress was enhanced in the cold adapted animals. RNA will be prepared with RNAqueous-Micro Isolation kit from Ambion (alternatively we can ship the tissues). We will pool samples from 4 rats per treatment to control for variability.
2007-09-28 | E-GEOD-2875 | biostudies-arrayexpress
Project description:Stress leads to important adaptive physiological responses including release of catecholamine from the adrenal medulla. Repeated or prolonged stess increses the propensity for many disorders including cardiovascular disease and neuropsychiatric disorders. The susceptibility to stress is determined by a number of factors including prior experience with stress. It has been found that while there is adaptation to prolonged cold stres; it leads to sensitization when cold stressed animals are exposed to a different (novel) stressor. Our study aims to determine the mechanis of this adaptatio and sensitization. We will determine teh gene expression patterns in rat adrenal medulla in response to severa times of cold stress. We will also determine the changes in gene expresion with single immobilization stress in adrenal medulla of rat with an dwithout preexposure to cold stress to investigate the mechanism of sensitizatio in cold adapted animals. We hypothesize that during the course of cold stess there are alterations in gene expression of several neurotransmitter related genes and transcription factors. In expression of several trascription factors, such as Fra-2 which lead to an exaggerated response to teh novel stresor. Rats were exposed to cold stress (4 degree C) for 1, 7, or 28 days. A parallel group was kept at room temperature (unstressed). Unstressed or rats preexposed to 28 days cold were immobilized for 2 hrs and killed by decapitation. The adrenal medullae, separatedly from right and left side, have been dissected and individually frozen at - 70 degree C. We will pool samples from 4 rats per treatment to control for variability.
2008-06-13 | E-GEOD-5033 | biostudies-arrayexpress
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArray＠ v1.
2014-10-15 | GSE57895 | GEO
Project description:While cold stress has been shown to seriously impact cattle industry, there are only a few reports investigating the effect of cold stress on cattle. Whether severe cold stress results in alterations in gene expression and affects molecular genetic mechanisms remains unknown. We used microarrays to analyze the alterations in gene expression in peripheral blood samples in response to cold exposure and identified differentially regulated genes. This study was performed on 30 healthy Sanhe heifers with similar genetic backgrounds, weight, and age. In order to induce cold stress, the cattle were transferred outdoor and were exposed to a temperature of -32°C for 3 hours followed by housing in cowshed at 5°C for 15 hours. Blood samples with EDTA were collected from each animal before and after the cold exposure. After total RNA was isolated from blood cells, six RNA samples (three derived before and three after the cold exposure), were collected from three animals randomly selected from the 30 healthy heifers for gene expression profiling in response to severe cold stress.
2016-04-02 | E-GEOD-79827 | biostudies-arrayexpress