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Items: 1 to 20 of 770

1.

Mechanistic Evaluation of Reduced Reproduction in Daphnia pulex Exposed to the Insensitive Munition, 1-methyl-3-nitro-1-nitroguanidine (MeNQ)

(Submitter supplied) The US Department of Defense (DOD) is developing insensitive munitions (IMs) that are resistant to unintended detonation to protect warfighters. To enable evaluation of the material life-cycle for the IM, 1-methyl-3-nitro-1-nitroguanidine (MeNQ), ecotoxicological impacts assessment was required. A previous investigation of MeNQ exposures in Daphnia pulex revealed concentration-responsive decreases in reproduction relative to controls (0 mg/L) across a 174, 346, 709, 1385, and 2286 mg/L exposure range. more...
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL29611
24 Samples
Download data: TXT
Series
Accession:
GSE164957
ID:
200164957
2.

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex

(Submitter supplied) Background Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female Daphnia can be genetically identical, yet display large differences in behaviour, morphology, lifespan and metabolic activity. Our goal was to integrate multiple omics datasets, including gene expression, splicing, histone modification and DNA methylation data generated from genetically identical female and male Daphnia pulex under controlled laboratory settings with the aim of achieving a better understanding of the underlying epigenetic factors that may contribute to the phenotypic differences observed between the two genders. more...
Organism:
Daphnia pulex
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL25991 GPL24021
31 Samples
Download data: FA, GFF, NARROWPEAK, TXT
Series
Accession:
GSE124427
ID:
200124427
3.

DNA methylation profiling of Daphnia species.

(Submitter supplied) To profile the Daphnia species methylome and to achieve a better understanding of the level of variations in the methylome of Daphnia species, we performed whole genome bisulfite sequencing (WGBSeq) of adult Daphnia magna Bham2 strain and Daphnia pulex Eloise Butler strain (EB45 and EB31 strains). We also analysed the correlation between gene expression and methylation in the two species, using data generated in this study and RNA-seq data from Orsini, et al. more...
Organism:
Daphnia pulex; Daphnia magna
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL24022 GPL24021 GPL23821
41 Samples
Download data: TXT, VCF
Series
Accession:
GSE103939
ID:
200103939
4.

Gene co-expression networks drive and predict reproductive effects in Daphnia in response to environmental disturbances

(Submitter supplied) ncreasing effects of anthropogenic stressors and those of natural origin on aquatic ecosystems have intensified the need for predictive and functional models of their effects. Here, we use gene expression patterns in combination with weighted gene co-expression networks and generalized additive models to predict effects on reproduction in the aquatic microcrustacean Daphnia. We developed models to predict effects on reproduction upon exposure to different cyanobacteria, different insecticides and binary mixtures of cyanobacteria and insecticides. more...
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL11278
335 Samples
Download data: PAIR
Series
Accession:
GSE102226
ID:
200102226
5.

Phenotypic plasticity of temperature induced Daphnia gene expression

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL11278
24 Samples
Download data: PAIR, TXT
Series
Accession:
GSE91031
ID:
200091031
6.

Phenotypic plasticity of temperature induced Daphnia gene expression; experiment 2

(Submitter supplied) This study measured the differential expression of genes from a single clonal Daphnia pulex isolate obtained from an eutrophic flooded opencast mine near Gräfenhain (Saxony, Germany) and has been kept in the laboratory since 2002. The daphniids (50 adult animals per batch) were raised in 3-L glass beakers under a 16 h:8 h L:D photoperiod. Three-quarter of the culture medium (M4) was renewed once a week, and the animals were equally fed ad libitum with algae (Desmodesmus subspicatus; SAG 53.80, Göttingen, Germany). more...
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL11278
12 Samples
Download data: PAIR, TXT
Series
Accession:
GSE91030
ID:
200091030
7.

Phenotypic plasticity of temperature induced Daphnia gene expression; experiment 1

(Submitter supplied) This study measured the differential expression of genes from a single clonal Daphnia pulex isolate obtained from an eutrophic flooded opencast mine near Gräfenhain (Saxony, Germany) and has been kept in the laboratory since 2002. The daphniids (50 adult animals per batch) were raised in 3-L glass beakers under a 16 h:8 h L:D photoperiod. Three-quarter of the culture medium (M4) was renewed once a week, and the animals were equally fed ad libitum with algae (Desmodesmus subspicatus; SAG 53.80, Göttingen, Germany). more...
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL11278
12 Samples
Download data: PAIR, TXT
Series
Accession:
GSE91025
ID:
200091025
8.

Temporal profiling and network analysis of rhythmic gene expression and novel functional gene annotation in the water flea, Daphnia pulex

(Submitter supplied) We analyzed genome-wide temporal transcriptional patterns from Daphnia pulex collected over a 48 hr time period using a cosine-fitting algorithm. Additionally, using a comprehensive network modeling and analysis approach, we go beyond the standard statistical analyses of the gene expression data. By doing so, we identified novel co-regulated rhythmic genes that have similar network topological as well as functional annotations as rhythmic genes identified by the statistical analyses but that cannot be identified by cosine-fitting alone. more...
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL20021
24 Samples
Download data: PAIR, TXT
Series
Accession:
GSE67781
ID:
200067781
9.

CAGE sequences from three developmental states in the microcrustacean Daphnia pulex.

(Submitter supplied) We report the application of CAGE (Cap Analysis of Gene Expression) on collections of Daphnia pulex individuals representing three major developmental states. This submission comes from a project of Michael Lynch and was funded by a grant from the National Institutes of Health entitled 'Population Genomics of Daphnia pulex' (Project Number: 1R01GM101672-01A1).
Organism:
Daphnia pulex
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19087
8 Samples
Download data: TXT
Series
Accession:
GSE80141
ID:
200080141
10.

Gene body methylation patterns in Daphnia are associated with gene family size

(Submitter supplied) We report the characterized gene body methylation patterns in two Daphnia species.
Organism:
Daphnia magna; Daphnia pulex
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL19087 GPL21075
6 Samples
Download data: TXT
Series
Accession:
GSE60475
ID:
200060475
11.

Daphnia miRNA expression data from Cadmium exposed and none-exposed samples

(Submitter supplied) We used Affymetrix microarrays to profile the Dapnia pulex miRNA expression under Cadmium exposure and identified Cadmium-responsive miRNAs
Organism:
Daphnia pulex; synthetic construct
Type:
Non-coding RNA profiling by array
Platform:
GPL19117
9 Samples
Download data: CEL
Series
Accession:
GSE68481
ID:
200068481
12.

Genetic and physiological mechanisms underlying genotype by dietary stoichiometry interactions in Daphnia

(Submitter supplied) Understanding the fitness consequences of correlated shifts in ecological parameters is a central challenge in contemporary biology. We studied two genotypes of the waterflea, Daphnia pulex that exhibit striking genotype x environment (GxE) interaction in response to shifts in phosphorus (P) supply, which also alters dietary carbon (C) content. Genotype1 (G1) had higher fitness under a LoC:HiP (C:P~100) diet, while Genotype2 (G2) performed better in C:P~800 diet. more...
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL11278
36 Samples
Download data: PAIR
Series
Accession:
GSE48233
ID:
200048233
13.

Identifying genes and pathways that respond differently to dietary C:P between old (~700-yr-old) and young (~10-yr-old) resurrected Daphnia pulicaria genotypes that differ in C and P physiology

(Submitter supplied) How does environmental change drive phenotypic evolution? We addressed this question using Daphnia genotypes separated by ~1600-years of evolution in a Minnesota lake using methods in resurrection ecology (i.e., reviving dormant eggs from sediments) and found substantial genetic and physiological differentiation. These shifts are highly correlated with anthropogenic environmental change, specifically phosphorus (P)-driven eutrophication. more...
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL11278
24 Samples
Download data: PAIR
Series
Accession:
GSE48232
ID:
200048232
14.

Expression analysis of kairomone responsive genes in Daphnia pulex

(Submitter supplied) Investigation of gene expression level changes in Daphnia pulex MFP strain between in the presence or absence of Chaoborus kairomone.
Organism:
Daphnia pulex
Type:
Expression profiling by genome tiling array
Platform:
GPL11278
12 Samples
Download data: PAIR
Series
Accession:
GSE63275
ID:
200063275
15.

Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia

(Submitter supplied) Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. more...
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL11278
40 Samples
Download data: PAIR
Series
Accession:
GSE62763
ID:
200062763
16.

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

(Submitter supplied) 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.
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL11278
36 Samples
Download data: PAIR, TXT
Series
Accession:
GSE53692
ID:
200053692
17.

Effects of microcystis on Daphnia pulex

(Submitter supplied) Although cyanobacteria produce a wide range of natural toxins that impact aquatic organisms, food webs and water quality, the mechanisms of toxicity are still insufficiently understood. Here, we implemented a whole-genome expression microarray to identify pathways, gene networks and paralogous gene families responsive to Microcystis stress in Daphnia pulex. Therefore, neonates of a sensitive isolate were given a diet contaminated with Microcystis to contrast with those given a control diet for sixteen days. more...
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL11278
4 Samples
Download data: TXT
Series
Accession:
GSE36635
ID:
200036635
18.

How do consumers deal with stoichiometric constraints?

(Submitter supplied) Determine gene expression in daphnia exposed to biotic and abiotic stressors. Identify in Daphnia pulex unique gene regulatory patterns involved in the regulation of limited phosphorous.
Organism:
Daphnia pulex
Type:
Expression profiling by array
Platform:
GPL13280
4 Samples
Download data: GPR
Series
Accession:
GSE27959
ID:
200027959
19.

Daphnia ecotypes fed lab versus natural resources

(Submitter supplied) Consumer-resource interactions are a central issue in evolutionary and community ecology because they play important roles in selection and population regulation. Most consumers encounter resource variation at multiple scales, and respond through phenotypic plasticity in the short term or evolutionary divergence in the long term. The key traits for these responses may influence resource acquisition, assimilation and/or allocation. more...
Organism:
Daphnia pulex; Daphnia pulicaria
Type:
Expression profiling by array
Platform:
GPL13280
16 Samples
Download data: GPR, TXT
Series
Accession:
GSE31001
ID:
200031001
20.

Empirical Annotation of the Daphnia pulex genome; Experiment C

(Submitter supplied) Experiments conducted on this tiling array are used to (1) validate the frozen gene sets of the current genome annotation, (2) improve the predicted gene structures by empirically determining UTRs and intron-exon boundaries, identifying missing upstream, internal, and downstream exons and alternative transcripts, (3) propose gene structure models in transcribed regions containing no predicted genes and (4) delineate transcriptionally active regions of the genome from intergenic, intronic and genic regions. more...
Organism:
Daphnia pulex
Type:
Expression profiling by genome tiling array
Platforms:
GPL11200 GPL11201
6 Samples
Download data: PAIR
Series
Accession:
GSE25856
ID:
200025856
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