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) 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) 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) 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) 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 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; Dictyostelium discoideum AX4

Type:

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

4 related Platforms

117 Samples

Download data: H5, NARROWPEAK

(Submitter supplied) The goal of RNA-seq is to identify the differential expressed genes in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Two biological replicates were assigned for each group and in total 8 groups were prepared for RNA-seq libraries with 500 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26360

8 Samples

Download data: H5, XLSX

(Submitter supplied) We report the chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) on H3, H3K4me1, H3K4me3, H3K9me3, H3K27ac, H3K27me3, and H3K36me3. ChIP-seq were sequenced to a depth of at least 8 million total reads/sample. We found that H3K4me3, H3K27ac and H3K4me1 show separation between unicellular and multicellular stages in principal component analysis (PCA); other marks were unable to show a clear separation in PCA.

Organism:

Dictyostelium discoideum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26360

64 Samples

Download data: NARROWPEAK

(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). Two biological replicates were assigned for each group and in total 8 groups were prepared for ATAC-seq libraries. We mapped about 10 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:

GPL26360

8 Samples

Download data: NARROWPEAK

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

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26668 GPL29548

46 Samples

Download data: MTX, TSV

(Submitter supplied) Dictyostelium discoideum behavior depends on nutrients1. When sufficient food is present these amoebae exist in a unicellular state, but upon starvation they aggregate into a multicellular organism2,3. This unique biology makes D. discoideum an ideal model for investigating how fundamental metabolic pathways command cell differentiation and function. We show here that reactive oxygen species (ROS), generated as a consequence of nutrient limitation, lead to the sequestration of the amino acid cysteine in the antioxidant glutathione, limiting the use of its sulfur atom for processes such as protein translation and FeS cluster-containing enzyme activity that contribute to mitochondrial metabolism and cellular proliferation. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26668

4 Samples

Download data: MTX, TSV

(Submitter supplied) Dictyostelium discoideum behavior depends on nutrients1. When sufficient food is present these amoebae exist in a unicellular state, but upon starvation they aggregate into a multicellular organism2,3. This unique biology makes D. discoideum an ideal model for investigating how fundamental metabolic pathways command cell differentiation and function. We show here that reactive oxygen species (ROS), generated as a consequence of nutrient limitation, lead to the sequestration of the amino acid cysteine in the antioxidant glutathione, limiting the use of its sulfur atom for processes such as protein translation and FeS cluster-containing enzyme activity that contribute to mitochondrial metabolism and cellular proliferation. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29548

42 Samples

Download data: TSV, TXT