GEO DataSets

(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) 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; 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) 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) The social amoeba Dictyostelium discoideum integrates into a multicellular organism when individual starving cells aggregate and form a mound. The cells then integrate into defined tissues and develop into a fruiting body that consists of a stalk and spores. Aggregation is initially orchestrated by waves of extracellular cyclic adenosine monophosphate (cAMP) and previous theory suggested that cAMP and other field-wide diffusible signals mediate tissue integration and terminal differentiation as well. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9379

12 Samples

Download data: TXT

(Submitter supplied) Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. more...

Organism:

Dictyostelium discoideum AX2

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24705 GPL24706

16 Samples

Download data: TXT

(Submitter supplied) We identified 3418 genes transcribed at a level of at least two copies each. We identified many transcripts involved in protein translation, cell maintenance and metabolism, as expected for vegetative cells. The most highly expressed cell signaling genes include ubiquitin, smlA, and nucleotide exchange factors RasGEF F and Ras GEF G. Additionally, we identified many genes previously reported to be expressed only during later stages of development including dutA, actin8, thioredoxin3, culmination specific protein 45D, discoidin II and yelA. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by SAGE

Platform:

GPL7037

1 Sample

Download data

(Submitter supplied) DNA methylation has been shown to act by directly modulating transcription factor affinity to DNA binding sites and by recruiting methyl-CpG binding proteins, which form complexes with histone deacetylases (HDACs). Both mechanisms can affect gene regulation, but the extent to which HDACs contribute to the function of DNA methylation and transcription factor occupancy is not clear. To address this question we measured gene expression alterations, chromatin accessibility and transcription factor occupancy in wild type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing

Platforms:

GPL13112 GPL21103

126 Samples

Download data: BW, TXT

(Submitter supplied) Cross species comparison of genomes and transcriptomes is a powerful tool for understanding underlying biological processes, accurate functional classification of genes, and discovery of novel elements. The shift to next-generation sequencing platforms has tremendously accelerated the analysis of genomes and transcriptomes. The use of this technology for transcriptome analysis has many advantages over hybridization based technologies, including higher sensitivity and specificity, and eliminates the need for probe design. more...

Organism:

Dictyostelium purpureum; Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9379 GPL9380

36 Samples

Download data: TXT

(Submitter supplied) Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into fully integrated multicellular organisms. Early phases of the developmental program are often studied in cells starved in suspension while cAMP is provided exogenously. more...

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9379

67 Samples

Download data: TXT

(Submitter supplied) In many developmental systems, morphogenesis is coupled with dramatic changes in spatiotemporal gene expression, often orchestrated by the coordinated action of transcription factors. Development of the social soil amoebae Dictyostelium discoideum proceeds through a sequence of morphological and transcriptional changes, but the role of transcription factors in development is not well understood. GtaC, a GATA-type zinc-finger transcription factor, is essential for Dictyostelium development. more...

Organism:

Dictyostelium discoideum

Type:

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

Platform:

GPL9379

26 Samples

Download data: TXT

(Submitter supplied) The Nucleosome Remodeling and Deacetylase (NURD) complex is a key regulator of cell differentiation that has also been implicated in tumorigenesis. Loss of the NURD subunit DOC1 is associated with human oral squamous cell carcinomas (OSCC). Here, we show that restoration of DOC1 expression in OSCC cells leads to a reversal of epithelial-mesenchymal transition (EMT). This is caused by the DOC1-dependent recruitment of NURD to repress the Twist master regulators of EMT. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: NARROWPEAK

(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) How epigenetic information is transmitted from generation to generation remains largely unknown. Deletion of the C. elegans Histone H3 lysine 4 dimethyl (H3K4me2) demethylase spr-5 leads to inherited accumulation of the euchromatic H3K4me2 mark and progressive decline in fertility. Here we identified a genetic network of chromatin-modifying factors, including the H3K4me1/me2 methyltransferases SET-17 and SET-30, the H3K9me1/me2 methyltransferase MET-2, an H3K9me3 methyltransferase, SET-26, the H3K9me3 demethylase JMJD-2, and an H3K9me reader EAP-1, which regulate the trans-generational flow of epigenetic information. more...

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13657

14 Samples

Download data: BED

(Submitter supplied) We describe the gene expression pattern of a Dictyostelium discoideum mutant depleted in the C-module-binding factor (CbfA) and autonomous gene-regulatory activities of CbfA carboxy-terminal domains (CbfA-CTDs)

Organism:

Dictyostelium discoideum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15643

12 Samples

Download data: TXT