GEO DataSets

(Submitter supplied) PRO-seq experiments in multiple organisms. Also, PRO-seq experiment of Nelfb and Nelfe degron mESC in serum/LIF with or without dTAG-13. 

Organism:

Escherichia coli; Mus musculus; Perkinsus marinus; Daphnia pulex; Strongylocentrotus purpuratus; Sphaeroforma arctica; Dictyostelium discoideum; Capsaspora owczarzaki; Creolimax fragrantissima; Haloferax mediterranei; Dryas iulia; Nematostella vectensis

Type:

Other

12 related Platforms

46 Samples

Download data

(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

(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

(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 magna; Daphnia pulex

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL24022 GPL24021 GPL23821

41 Samples

Download data: TXT, VCF

(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

(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

(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

(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

(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

(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

(Submitter supplied) We report the characterized gene body methylation patterns in two Daphnia species.

Organism:

Daphnia pulex; Daphnia magna

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL19087 GPL21075

6 Samples

Download data: TXT

(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

(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

(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

(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

(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

(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

(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

(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

(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