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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC63.2]

ABSTRACT: Dictyostelium discoideum, a microbial model for social evolution, is known to distinguish self from non-self and show genotype-dependent behavior during chimeric development. Aside from a small number of cell-cell recognition genes, however, little is known about the genetic basis of self/non-self recognition in this species. Based on the key hypothesis that there should be differential expression of genes if D. discoideum cells were interacting with non-clone mates, we performed transcriptomic profiling study in this species during clonal vs. chimeric development. Wild strains isolated from North Carolina, which have been shown to form a dominance hierarchy when co-developing in chimeras, were used. The transcriptomic profiles of D. discoideum cells in clones vs. different chimeras were compared at five different developmental stages using a customized microarray. Effects of chimerism on global transcriptional patterns associated with social interactions were observed. The chimera developmental program may also provide insights on behavioral changes associated with social conflicts in this species. two-condition chimera experiments: two conditions (chimeric: NC105.1-RFP + NC63.2 vs. control: NC105.1-RFP + NC105.1), five time points for each condition (4 h, 8 h, 12 h, 16 h, and 20 h), two biological replicates for each condition at each time point, two technical replicates for each biological replicate (Cy5 vs. Cy3)

ORGANISM(S): Dictyostelium discoideum

SUBMITTER: Si Li

PROVIDER: E-GEOD-57210 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC28.1]

Project description:Dictyostelium discoideum, a microbial model for social evolution, is known to distinguish self from non-self and show genotype-dependent behavior during chimeric development. Aside from a small number of cell-cell recognition genes, however, little is known about the genetic basis of self/non-self recognition in this species. Based on the key hypothesis that there should be differential expression of genes if D. discoideum cells were interacting with non-clone mates, we performed transcriptomic profiling study in this species during clonal vs. chimeric development. Wild strains isolated from North Carolina, which have been shown to form a dominance hierarchy when co-developing in chimeras, were used. The transcriptomic profiles of D. discoideum cells in clones vs. different chimeras were compared at five different developmental stages using a customized microarray. Effects of chimerism on global transcriptional patterns associated with social interactions were observed. The chimera developmental program may also provide insights on behavioral changes associated with social conflicts in this species. two-condition chimera experiments: two conditions (chimeric: NC105.1-RFP + NC28.1 vs. control: NC105.1-RFP + NC105.1), five time points for each condition (4 h, 8 h, 12 h, 16 h, and 20 h), two biological replicates for each condition at each time point, two technical replicates for each biological replicate (Cy5 vs. Cy3)

2014-05-01 | E-GEOD-57209 | biostudies-arrayexpress

Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC85.2]

Project description:Dictyostelium discoideum, a microbial model for social evolution, is known to distinguish self from non-self and show genotype-dependent behavior during chimeric development. Aside from a small number of cell-cell recognition genes, however, little is known about the genetic basis of self/non-self recognition in this species. Based on the key hypothesis that there should be differential expression of genes if D. discoideum cells were interacting with non-clone mates, we performed transcriptomic profiling study in this species during clonal vs. chimeric development. Wild strains isolated from North Carolina, which have been shown to form a dominance hierarchy when co-developing in chimeras, were used. The transcriptomic profiles of D. discoideum cells in clones vs. different chimeras were compared at five different developmental stages using a customized microarray. Effects of chimerism on global transcriptional patterns associated with social interactions were observed. The chimera developmental program may also provide insights on behavioral changes associated with social conflicts in this species. two-condition chimera experiments: two conditions (chimeric: NC105.1-RFP + NC85.2 vs. control: NC105.1-RFP + NC105.1), five time points for each condition (4 h, 8 h, 12 h, 16 h, and 20 h), two biological replicates for each condition at each time point, two technical replicates for each biological replicate (Cy5 vs. Cy3)

2014-05-01 | E-GEOD-57211 | biostudies-arrayexpress

Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC85.2]

2014-05-01 | GSE57211 | GEO

Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC63.2]

2014-05-01 | GSE57210 | GEO

Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum [NC105.1_RFP_vs_NC28.1]

2014-05-01 | GSE57209 | GEO

Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-05-01 | E-GEOD-57212 | biostudies-arrayexpress

RNA-Seq data of terminal differentiated cells in Dictyostelium discoideum

Project description:The intent of the experiment was to gather transcriptomic data from terminally differentiated cell types --spore, stalk, and cup cells-- in a simple multicellular model system, Dictyostelium discoideum, in order to characterize the cell-type specific gene expression patterns. Specifically, we dissociated and collected each cell type from the fruiting bodies of D. discoideum at 24 hours of development. We also collected exponentially growing vegetative cells of D. discoideum.

2019-01-31 | E-MTAB-7215 | biostudies-arrayexpress

The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium

Project description: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. It decodes pulsatile extracellular cAMP signals during early development and mediates cell-type differentiation at later stages. Here, we studied the developmental regulatory roles of GtaC through the concerted analysis of temporal ChIP- and RNA-sequencing data from strains that carry different alleles of gtaC. We show that GtaC exhibits temporally distinctive DNA-binding patterns throughout early development, accompanied by largely cotemporaneous expression of its target genes. We also show that GtaC binds DNA in two modes. One of these modes exhibits binding preferences for canonical GATA-like sequences, the regulatory consequences accompanying which is predominantly up-regulation of target gene expression. The other binding mode is mostly associated with down-regulation. Among its targets we find transcription factors that are essential for development as well as genes involved in cAMP signaling and cell-type specification. Our results suggest that GtaC is a master regulator that regulates multiple physiological processes during early development, when Dictyostelium transitions from a group of unicellular amoebae to an integrated multicellular organism. Cotemporaneous transcriptional profiling and ChIP sequencing during early Dictyostelium development

2015-07-02 | E-GEOD-63151 | biostudies-arrayexpress

abc transporters in Dictyostelium discoideum development

Project description:ATP-binding cassette (ABC) transporters can translocate a broad spectrum of molecules across the cell membrane including physiological cargo and toxins. ABC transporters are known for the role they play in resistance towards anticancer agents in chemotherapy of cancer patients. There are 68 ABC transporters annotated in the genome of the social amoeba Dictyostelium discoideum. We have characterized more than half of these ABC transporters through a systematic study of mutations in their genes. We have analyzed morphological and transcriptional phenotypes for these mutants during growth and development and found that most of the mutants exhibited rather subtle phenotypes. A few of the genes may share physiological functions, as reflected in their transcriptional phenotypes. Since most of the abc-transporter mutants showed subtle morphological phenotypes, we utilized these transcriptional phenotypes to identify genes that are important for development by looking for transcripts whose abundance was unperturbed in most of the mutants. We found a set of 668 genes that includes many validated D. discoideum developmental genes. We have also found that abcG6 and abcG18 may have potential roles in intercellular signaling during terminal differentiation of spores and stalks. Transcriptional phenotyping during development of abc transporter mutants in Dictyostelium discoideum

2013-06-14 | E-GEOD-45555 | biostudies-arrayexpress

The intrinsic and extrinsic effects of Tet proteins during gastrulation

Project description:To isolate cell-autonomous effects of TET loss during gastrulation, we utilized a chimeric embryo platform in which fluorescently tagged Tet-deficient and control mouse embryonic stem cells (mESCs) were either injected into tetraploid (4N) or diploid (2N) blastocysts, and allowed to develop in utero. In 4N complemented embryos, the resulting embryonic compartment is solely comprised of the injected mESCs derivatives (hereinafter denoted as whole-embryo chimera), whereas in chimeras obtained using 2N host blastocysts, the embryonic compartment contains both wild-type (WT) and injected cell derivatives (hereinafter denoted as mixed chimera). We performed single-cell RNA-seq for each whole-embryo and mixed chimera embryo, and compared the transcriptomes to a defined single-cell/single-embryo atlas. We further performed methylation analysis using post-bisulfite adaptor tagging (PBAT) for sorted Tet-TKO mutant and control from E8.5 mixed chimeras. Our work demonstrates an unbiased approach for defining intrinsic and extrinsic embryonic gene function based on temporal differentiation atlases, and disentangles the intracellular effects of the demethylation machinery from its broader tissue-level ramifications.

2022-06-14 | GSE205917 | GEO

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