GEO DataSets

(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 use a custom microarray for the crustacean Daphnia pulex to investigate gene expression in males, juvenile females and pregnant females. Keywords: sex-biased, developmental

Organism:

Daphnia pulex

Type:

Expression profiling by array

Platform:

GPL4349

8 Samples

Download data: GPR

(Submitter supplied) The selection and activity of transcription start sites (TSSs) are central to gene regulation and depend on sequence and chromatin features within a core promoter region. We present, at single-bp resolution, the TSS landscape of Oikopleura dioica, a marine chordate in the sister group to vertebrates and relate dynamics of promoter usage, and their architectures, across its life cycle, to chromatin features. more...

Organism:

Oikopleura dioica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17726

6 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) 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) The lack of a comprehensive map of transcription start sites in Toxoplasma gondii has impeded advances in decrypting the molecular mechanisms underlying the regulation of gene expression. Genome-wide approaches for mapping transcription initiation have been instrumental in defining the determinants of transcription initiation in a range of model eukaryotes. We used a protocol for 5′-end RNA sequencing, called RAMPAGE, to sequence the 5′-ends of capped mRNA from ME49 and RH tachyzoites, as well as from ME49 bradyzoites. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25973

6 Samples

Download data: BEDGRAPH

(Submitter supplied) Sequencing of 5' ends of RNA molecules from control and exosome-depleted S2 cells.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

8 Samples

Download data: BED

(Submitter supplied) Genome-wide mapping of the TSS in root and shoot from two maize lines B73 and A632 Genome-wide locations and dynamics of maize core promoters obtained from the experimental establishment of the TSSs coordinates. The work derived from this data it is the first genome-wide atlas of core promoters and its dynamic generated for an important crop species.

Organism:

Zea mays subsp. mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17914

8 Samples

Download data: BED, CSV

(Submitter supplied) Quantify gene expression by measurement of mRNA in maize inbred line Mo17 mRNA-seq used as part of the validation of CAGE results used for the genome-wide location and dynamic of maize core promoters obtained from the experimental establishment of the TSSs coordinates

Organism:

Zea mays subsp. mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17914

4 Samples

Download data: FPKM_TRACKING, GTF, TXT

(Submitter supplied) We present Smart-Seq2 Rolling Circle to Concatemeric Consensus (Smar2C2) for the identification and quantification of transcription start sites. Smar2C2 allows for the identification of upwards of 70 million unique transcription start sites from a single sample with as little as 40 pg of RNA input.

Organism:

Oryza sativa; Sorghum bicolor; Zea mays; Glycine max; Triticum aestivum

Type:

Other

5 related Platforms

46 Samples

Download data: 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) To study the function of this residue independent from the enzymes that modify it, we used a “histone replacement” system in Drosophila to generate a non-modifiable H3K36 lysine-to-arginine (H3K36R) mutant. Post-translational modification of histone H3K36 is neither required to suppress cryptic transcription initiation nor to include alternative exons in Drosophila; instead it promotes expression of active genes by stimulating polyadenylation.

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL19132 GPL16479 GPL13304

52 Samples

Download data: BED, BW, DIFF

(Submitter supplied) Background: During the symbiosis with legumes, Bradyrhizobium japonicum cells infect roots where they induce the formation of root nodules and differentiate into intracellular nitrogen-fixing bacteroids. We used differential RNA-seq (dRNA-seq) for the genome-wide detection of transcriptional start sites (TSSs) in B. japonicum USDA 110 cells grown free-living or as bacteroids in soybean root nodules. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20219

4 Samples

Download data: WIG

(Submitter supplied) We provide a comprehensive map of transcription start sites (TSSs) for HBV at single nucleotide resolution using CAGE.

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL13112

11 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11203 GPL13304 GPL10999

37 Samples

Download data: BED, BW

(Submitter supplied) Since their discovery, transposable elements have been proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, in particular by providing transcription start sites (TSSs) for host genes. To investigate their contribution to developmental gene expression, we developed RAMPAGE, a high-throughput 5'-complete cDNA sequencing approach to accurately discover TSSs, characterize their transcripts, and quantify their expression. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13304 GPL11203

36 Samples

Download data: BED, BW, TXT

(Submitter supplied) 5'-complete cDNA sequencing on ribosome-depleted total RNA from the human K562 cell line. Provides high-quality, genome-wide single-base resolution profiling of transcription start sites and their expression levels.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

1 Sample

Download data: BED, BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Klebsiella pneumoniae subsp. pneumoniae MGH 78578; Klebsiella pneumoniae; Escherichia coli K-12

Type:

Expression profiling by array; Expression profiling by high throughput sequencing; Other

Platforms:

GPL15233 GPL15223 GPL15232

6 Samples

Download data: PAIR