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Items: 1 to 20 of 2599

1.

Collective oscillatory signaling acts as a developmental timer initiated by weak coupling of a noisy pulsatile signal

(Submitter supplied) Oscillatory phenomena are ubiquitous across different biological scales, from individual cells to tissues and whole organisms. In physical systems, oscillatory behaviour can emerge from weak coupling of independent stochastic elements. Once established, oscillations can drive coordinated group behaviour and encode robust information through oscillation frequency or amplitude. Here we use experimentation and modelling to understand the emergence and information coding properties of oscillatory cyclic adenosine monophosphate (cAMP) signaling in D. more...
Organism:
Dictyostelium discoideum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26000
30 Samples
Download data: TXT
Series
Accession:
GSE272520
ID:
200272520
2.

Multi-omics analysis of aggregative multicellularity

(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
Series
Accession:
GSE249880
ID:
200249880
3.

Pol II pausing is a milestone on the road to complex animals

(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:
Haloferax mediterranei; Dryas iulia; Nematostella vectensis; Escherichia coli; Mus musculus; Perkinsus marinus; Dictyostelium discoideum; Capsaspora owczarzaki; Creolimax fragrantissima; Daphnia pulex; Strongylocentrotus purpuratus; Sphaeroforma arctica
Type:
Other
12 related Platforms
46 Samples
Download data
Series
Accession:
GSE223913
ID:
200223913
4.

Collective signalling drives rapid jumping between cell states

(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
Series
Accession:
GSE220242
ID:
200220242
5.

Functional Characterisation of the Core Autophagy Protein ATG5 in Dictyostelium discoideum

(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
Series
Accession:
GSE142251
ID:
200142251
6.

Effects of knocking down RNP1A on gene expression in Dictyostelium discoideum

(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
Series
Accession:
GSE207131
ID:
200207131
7.

The 2´-O-methylation landscape of ribosomal RNA in Dictyostelium discoideum 

(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
Series
Accession:
GSE186560
ID:
200186560
8.

RNA-Seq analysis of wild-type and mutant D. discoideum amebae

(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
Series
Accession:
GSE156813
ID:
200156813
9.

RNA-Seq analysis of wild-type and ttpA-C240ins mutant D. discoideum amebae in surface and liquid growth

(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
Series
Accession:
GSE156812
ID:
200156812
10.

RNA-Seq analysis of wild-type and ttpA-C240ins mutant D. discoideum amebae during short-term nutrient deprivation

(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
Series
Accession:
GSE156811
ID:
200156811
11.

RNA-Seq analysis of wild-type and ttpA-D450trx mutant D. discoideum amebae

(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
Series
Accession:
GSE156810
ID:
200156810
12.

RNA-Seq analysis of wild-type and ttpA-C231S, ttpA-E236fsx, and ttpA-Y242fsx mutant D. discoideum amebae

(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
Series
Accession:
GSE156809
ID:
200156809
13.

Transcriptional milestones in Dictyostelium development

(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 GPL22784 GPL26668
486 Samples
Download data: TAB, XLSX
Series
Accession:
GSE152851
ID:
200152851
14.

RNAseq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16

(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
Series
Accession:
GSE162070
ID:
200162070
15.

Single-cell transcriptome analysis in D. discoideum (AX4) in different developmental stages

(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
Series
Accession:
GSE153795
ID:
200153795
16.

Chromatin accessibility in D. discoideium (AX4) in different developemental stages [ATAC-seq II]

(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
Series
Accession:
GSE153733
ID:
200153733
17.

Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium

(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
Series
Accession:
GSE137604
ID:
200137604
18.

Transcriptome analysis in D. discoideium (AX2) in different developmental stages

(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
Series
Accession:
GSE137602
ID:
200137602
19.

Determine the genome-wide localization of histone and histone marks in different stages of D. discoideum

(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
Series
Accession:
GSE137599
ID:
200137599
20.

Chromatin accessibility in D. discoideium (AX2) in different developmental stages

(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
Series
Accession:
GSE137598
ID:
200137598
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