Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia

ABSTRACT: In this study we use nimblegen high-density arrays to examine gene expression regulation in a common-garden experiment varying thermal environments. We report genome-wide patterns of gene expression in two heat tolerant southern and two heat-sensitive northern clones of Daphnia pulex exposed to either optimal (18°C) or substressful (28°C) temperatures. Four competitive hybridizations of heat tolerant clones BW102 (hereafter B) and KSP3 (hereafter K), and heat sensitive clones EB1 (hereafter E) and CHQ3 (hereafter C) in response to thermal stress of either 18 degrees Celcius (here after 18) or 28 degrees (hereafter 28) in a loop design where each hybridization was replicated four times with two dye-swaps nested in each set of replicates.

ORGANISM(S): Daphnia pulex

SUBMITTER: Jacqueline Lopez

PROVIDER: E-GEOD-53692 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia

Project description:In this study we use nimblegen high-density arrays to examine gene expression regulation in a common-garden experiment varying thermal environments. We report genome-wide patterns of gene expression in two heat tolerant southern and two heat-sensitive northern clones of Daphnia pulex exposed to either optimal (18°C) or substressful (28°C) temperatures.

2014-10-02 | GSE53692 | GEO

Locally adapted populations of a copepod species exhibit starkly different gene expression responses to different thermal environments

Project description:This study aimed at measuring transcriptome-wide gene expression in four populations of the copepod T. californicus. Populations were exposed to two different thermal regime, a variable 20-28 degree and a constant 20 degree followed by a one-time stress at 28 degrees. RNA was extracted at 20 and 28 degrees for all populations from all thermal regimes. Transcriptome-wide gene expression was measured, and differentially expressed genes were determined for all populations for the different temperature combinations. The results show that each populations responds to the changes in temperature in a drastically different manner (in terms of gene expression), which can have implications regarding the way these and other organisms will respond to climate change. Two southern and two northern populations of Tigriopus californicus were exposed to a variable 20-28 degree and a constant 20 degree followed by a one-time stress at 28 degrees. RNA was extracted at 20 and 28 degrees for all populations from all thermal regimes. mRNA profiles were generated by 100bp single end sequencing in the Illumina HiSeq 2000 and 2500, with one replicate per population per treatment.

2016-07-25 | E-GEOD-80737 | biostudies-arrayexpress

Locally adapted populations of a copepod species exhibit starkly different gene expression responses to different thermal environments

2016-07-25 | GSE80737 | GEO

Assessment of Thermotolerance in preshocked hsp70(-/-) and (+/+) cells

2009-04-09 | GSE11120 | GEO

Proteomic characteristics of hepatopancreas in cold-tolerant families and common families of Litopenaeus vannamei

Project description:In this study, hepatopancreas tissues of cold-tolerant and common families of Litopenaeus vannamei were selected by the Guangxi Academy of Fishery Sciences for proteomic study. Hepatopancreas were treated at 28℃, 18℃ and 10℃ respectively based on DIA technology. There were three replicates of cold-tolerant families and common families at 28℃, 18℃ and 10℃ respectively, and each replicate contained hepatopancreas mixed samples of 6 shrimp at random. A total of 18 samples were analyzed. The original data of common families at 28℃, 18℃ and 10℃ were named Lv-C-28、Lv-C-18 and Lv-C-10 respectively, while the original data of cold-tolerant families at 28℃, 18℃ and 10℃ were named Lv-T-28、Lv-T-18 and Lv-T-10 respectively.

2023-06-09 | PXD041965 |

Expression data from the subclones of Lewis Lung Carcinoma (LLC) cells

Project description:Medium conditioned by LLC cells stimulates thermogenic gene expression when added onto primary adipocytes. We generated single cell colonies from parental LLC cells. Media conditioned by the subclones stimulated thermogenic gene expression in primary adipocytes at varying degrees. Subclones 2, 3, 6 and 28 produce significantly larger amount of thermogenic activity than the subclones 18, 19, 23 and 24. We compared gene expression profiles of these subclones to identify secreted factors enriched in the more thermogenic clones.

2014-07-13 | GSE57797 | GEO

Maternal Cold Exposure Enhances Fetal Brown Adipose Tissue Development

Project description:Brown adipose tissue (BAT) is specialized for dissipating energy in the form of heat. BAT-mediated heat production is critical for effective adaption of newborns to the extrauterine environment. However, very little is known about whether and how fetal BAT development is modulated in-utero in response to changes in maternal thermal environment during pregnancy. The present study aims at determining whether maternal cold exposure influences fetal BAT development via placental remodeling. BL6 female mice were acclimated at 28C or 18C for 7 days prior to mating with male mice and maintained at their respective temperature until embryonic day 18.5. Placental and fetal BAT samples were collected for transcriptome analysis.

2021-06-18 | GSE151905 | GEO

Transcriptional profiling by array to characterize temperature stress responses in larval zebrafish

Project description:96 hpf zebrafish larvae were exposed to cold (16 degrees C) or heat (34 degrees C) stress for 2, 12, 24 and 48h. Time-matched controls were maintained at 28 degrees C. The transcriptional responses elicited by temperature stress in larval zebrafish were investigated by microarray.

2012-02-01 | E-MTAB-826 | biostudies-arrayexpress

Transcription profiling of mouse preshocked hsp70(-/-) and (+/+) cells to assess thermotolerance

Project description:From preliminary experiments, HSP70 deficient MEF cells display moderate thermotolerance to a severe heatshock of 45.5 degrees after a mild preshock at 43 degrees, even in the absence of hsp70 protein. We would like to determine which genes in these cells are being activated to account for this thermotolerance. Experiment Overall Design: Two cell lines are analyzed - hsp70 knockout and hsp70 rescue cells. 6 microarrays from the (-/-)knockout cells are analyzed (3 Pretreated vs 3 unheated controls). For the (+/+) rescue cells, 4 microarrays are used (2 pretreated and 2 unheated controls). Cells were plated at 3k/well in a 96 well plate, covered with a gas permeable sealer and heat shocked at 43degrees for 30 minutes at the 20 hr time point. The RNA was harvested at 3hrs after heat treatment.

2009-04-17 | E-GEOD-11120 | biostudies-arrayexpress

Integrated analysis of circRNA-miRNA-mRNA ceRNA network responses to heat stress in rainbow trout (Oncorhynchus mykiss) liver

Project description:With the intensification of global warming, rainbow trout is suffering from varying degrees thermal stimulation, heat stress may cause pathological signs or diseases by reducing the immune roles and then lead to mass mortality, so high temperatures severely restrict the development of its aquaculture. Understanding the molecular regulation mechanism of rainbow trout under heat stress is used to take measures to relieve symptoms. We performed multiple transcriptomic analysis of liver tissues from rainbow trout under heat stress (24 °C) and control conditions (18 °C) to identify circRNAs, miRNAs and mRNAs. Changes of non-specific immune parameters revealed that strong stress response of rainbow trout is caused in 24 °C. A total of 324 DEcircRNAs, 105 DEmiRNAs, and 1885 DEmRNAs were identified from six libraries, and ceRNA regulatory network is constructed. 301 circRNA–miRNA and 51 miRNA–mRNA negative correlation pairs were screened from ceRNA regulatory network, and predicted three regulatory correlation pairs that novel_circ_003889 - novel-m0674-3p - hsp90ab1, novel_circ_002325 - miR-18-y - HSPA13 and novel_circ_002446 - novel-m0556-3p - hsp70. Some genes involved in metabolic process, biological regulation or response to stimulus are highly induced at high temperatures. Several important pathways involved in heat stress were characterized, such as Protein processing in endoplasmic reticulum (ER), Estrogen signaling pathway, HIF-1 signaling pathway, etc. These results extend our understanding of the molecular mechanisms of heat stress response and expected to provide a novel insight into develop strategies for relieve heat stress.

2019-11-08 | GSE140112 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data