GEO DataSets

(Submitter supplied) The extent to which mRNA and protein levels correlate is still not fully known, especially during development, when cells undergo a major transition in gene expression. One organism with particular development is Dictyostelium discoideum, during which it transitions from free-living unicellular to multicellular. Previously the transcriptome has been thoroughly studied during multicellular development, however the proteome and its correlation to the transcriptome during this transition is not fully understood. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26668

24 Samples

Download data: TXT

(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:

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

Type:

Other

12 related Platforms

46 Samples

Download data

(Submitter supplied) A continuous single cell transcriptomic time course of Dictyostelium discoideum early development.

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26360

2 Samples

Download data: CSV

(Submitter supplied) The human protozoan parasiteEntamoeba histolyticais responsible for amebiasis, a disease endemic to developing countries.E. histolyticatrophozoites colonize the large intestine, primarily feeding on bacteria. However, in the GI, as well as in aquatic and soil microenvironments, bacterial cells form aggregates or structured communities, called biofilm, too large for phagocytosis. However, trophozoites are still able to invade and degrade bacteria under biofilm form by a mechanism mimicking digestive exophagy. more...

Organism:

Entamoeba histolytica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33438

9 Samples

Download data: CSV, TXT, XLSX

(Submitter supplied) Amebiasis is caused by the protozoan parasite Entamoeba histolytica. Treatment options other than metronidazole and its derivatives are few, and their low efficacy against asymptomatic cyst carriers, and experimental evidence of resistance in vitro justify the discovery/repurposing campaign for new drugs against amebiasis. To better understand the role of glycerol metabolism in this parasite, we focused on characterizing two important enzymes, glycerol kinase (GK) and glycerol 3-phosphate dehydrogenase (G3PDH). more...

Organism:

Entamoeba histolytica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33319

9 Samples

Download data: TXT, XLSX

(Submitter supplied) Purpose: Global survey of the transcriptome in autophagy-deficient strains of D. discoideum Results: Our RNAseq analysis of ATG5‾, ATG5‾/12‾ and ATG5‾/12‾/16‾ cells revealed major transcriptional changes in a large number of genes in comparison to AX2 Conclusions: Our study presents a first detailed analysis of the transcriptome in autophagy-deficient strains of D. discoideum. The data were generated by RNA-seq technology. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26000

24 Samples

Download data: TSV

(Submitter supplied) To investigate the function of RNP1A, an RNA-binding protein in Dictyostelium discoideum

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26668

8 Samples

Download data: TXT

(Submitter supplied) In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleated syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters, and if nuclei within the cell diversify into heterogeneous states. more...

Organism:

Physarum polycephalum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30072

949 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was applied to study methylation patterns in Dictyostelium discoideum

Organism:

Dictyostelium discoideum

Type:

Other

Platform:

GPL30893

2 Samples

Download data: XLSX

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

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26668 GPL26000

83 Samples

Download data

(Submitter supplied) In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain. This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain. We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26668

24 Samples

Download data: TXT

(Submitter supplied) In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain. This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain. We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26000

35 Samples

Download data: TXT

(Submitter supplied) In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain. This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain. We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26668

8 Samples

Download data: TXT

(Submitter supplied) In many eukaryotes, mRNAs containing specific AU-rich motifs are regulated by proteins of the tristetraprolin (TTP) family, which bind to these motifs through a tandem zinc finger (TZF) domain. This binding leads to promotion of subsequent deadenylation and decay, partly through a conserved carboxyl-terminal CNOT1 binding domain. We explored the physiological role of the single TTP family member (TtpA) expressed in Dictyostelium discoideum. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26668

16 Samples

Download data: TXT

(Submitter supplied) Purpose: Transcriptome characterization of Entamoeba histolytica trophozoites adapted to Auranofin Total RNA was extracted from control trophozoites (WT) and AFAT using the TRI reagent kit, according to the manufacturer instructions (Sigma-Aldrich USA). 6 RNAseq libraries were produced according to manufacturer protocol (NEBNext UltraII Directional RNA Library Prep Kit for Illumina, cat no. E7760) using 800ng total RNA. more...

Organism:

Entamoeba histolytica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30297

6 Samples

Download data: XLSX

(Submitter supplied) Dictyostelium development begins with single-cell starvation and ends with multicellular fruiting bodies. Developmental morphogenesis is accompanied by sweeping transcriptional changes, encompassing nearly half of the 13,000 genes in the genome. We performed time-series RNA-sequencing analyses of the wild type and 20 mutants to explore the relationships between transcription and morphogenesis,. These strains exhibit developmental arrest at different stages, accelerated development, or atypical morphologies. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL9379 GPL26668 GPL22784

486 Samples

Download data: TAB, XLSX

(Submitter supplied) Purpose: Global survey of the transcriptome and comparison to the proteome in autophagy-deficient strains of D. discoideum. Results: Our RNAseq analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells revealed major transcriptional changes in a large number of genes in comparison to AX2. Conclusions: Our study provides the first combined transcriptome and proteome analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells and adds to our knowledge of functions of these proteins in Dictyostelium discoideum.

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15643

36 Samples

Download data: XLS

(Submitter supplied) The goal of scRNA-seq is to identify the differential expressed genes in the wild-type D. discoideum at different developmental stages (vegetative, streaming, slug and fruiting bodies). Three biological replicates were assigned for each group and in total 12 groups were prepared for scRNA-seq libraries with 10000 cells as starting materials using Chromium Single Cell Gene Expression kit V3 (10x Genomics). more...

Organism:

Dictyostelium discoideum AX4

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28815 GPL28816

24 Samples

Download data: TSV

(Submitter supplied) The goal of ATAC-seq is to identify the open chromatin regions in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Three biological replicates were assigned for each group and in total 13 groups were prepared for ATAC-seq libraries. We mapped about 30 million reads per sample to D. discoideum with bowtie2 workflow. Open chromatin regions were deducted by ChIPseeker with corrected p < 0.05. more...

Organism:

Dictyostelium discoideum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26000

13 Samples

Download data: NARROWPEAK

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

Organism:

Dictyostelium discoideum AX4; Dictyostelium discoideum

Type:

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

4 related Platforms

117 Samples

Download data: H5, NARROWPEAK