DcgA knock-out experiment in Dictyostelium discoideum
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Dictyostelium discoideum
SUBMITTER: Reema Singh
PROVIDER: E-MTAB-3829 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
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
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
Project description:We utilized RNA-seq to profile expression levels in wild type AX2 cells and three mutants for the CHD family of ATP-dependent chromatin remodellers in Dictyostelium discoideum. Total RNA was polyA enriched and sequenced at two stages of development: in the growth stage (0H) and in 5H cAMP pulsed cells (5H). All mutants analysed were also in the AX2 background. Looking at mRNA levels in AX2, chdA-, chdB- and chdC-.
2014-01-03 | E-GEOD-47222 | biostudies-arrayexpress
Project description:Dictyostelium discoideum is an ideal organism to study SH2-domain mediated signal transduction because not only does it provide relatively simple model cell biological and developmental processes, but also possesses a highly streamlined repertoire of SH2-containing proteins. We studied one such novel protein, LrrB, by gene deletion and protein interaction experiments. A DNA microarray experiment carried out on growing cells reveals misregulation of a small set of vegetative genes in the lrrB knockout strain when compared to the parent, Ax2. Real time PCR experiments described in the accompanying manuscript extend these observations to show how this affects gene expression during early development, and that knockouts in another SH2 protein that interacts with LrrB show misregulation of some of the same genes, suggesting that these proteins may form part of a novel adaptor complex that regulates gene expression during Dictyostelium growth and early development.
2010-06-09 | E-TABM-803 | biostudies-arrayexpress
Project description: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. Cooperation between cells depends on an allorecognition system comprised of the polymorphic adhesion proteins TgrB1 and TgrC1. Binding between compatible TgrB1 and TgrC1 variants ensures that non-matching cells segregate into distinct aggregates prior to terminal development. Here, we have embedded a small number of cells with incompatible allotypes within fields of developing cells with compatible allotypes. We found that compatibility of the allotype encoded by the tgrB1 and tgrC1 genes is required for tissue integration, as manifested in cell polarization, coordinated movement, and differentiation into prestalk and prespore cells. Our results show that the molecules that mediate allorecognition in D. discoideum also control the integration of individual cells into a unified developing organism and this acts as a gating step for multicellularity. Total 12 samples were used for this analysis. 3 developmental timepoints were analyzed with 2 biological replication. And same 3 developmental timepoint of references (5 RNA mix) with 2 biological replication.
2016-04-13 | E-GEOD-68063 | biostudies-arrayexpress
Project description:Knockout mutants of polyketide synthase genes were generated (pks1, pks2, pks3, pks14, pks18, pks37) and compared to wild-type AX2 strain of Dictyostelium discoideum using Agilent custom microarrays. The Dictyostelium cells were harvested at eight developmental stages (Amoeboid, Intiation of starvation, loose aggregate, Streaming, Mound, Slug, early culminant, Fruiting body) and subjected to microarray based expression profiling.
2015-07-18 | GSE71036 | GEO
Project description:Label free interaction protoemics of Dictyostelium discoideum GFP-SAC1 compared to GFP expressing cells
2023-12-01 | PXD039848 | Pride
Project description: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. The optimised data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell. We conclude that RNA-seq based transcriptome characterisation would expedite genetic network analyses and permit the dissection of complex biologic functions.
2022-12-13 | GSE142251 | GEO
Project description:We report here that duplications of 15 kb or more are common in the genome of the social amoeba Dictyostelium discoideum. Most of the axenic "workhorse" strains Ax2 and Ax3/4 obtained from different laboratories can be expected to carry new duplications. The auxotrophic strains DH1 and JH10 also bear previously unreported duplications. Strain Ax3/4 is known to carry a large duplication on chromosome 2 and the domain boundary of this structure shows evidence of further instability; we find a further variable duplication on chromosome 5. These duplications are lacking in Ax2, which has instead a small duplication on chromosome 1. Stocks of the type isolate NC4 are similarly variable, though we have identified some approximating the assumed ancestral genotype. More recent wild-type isolates are almost without duplications, but we can identify small deletions or regions of high divergence, possibly reflecting responses to local selective pressures. Duplications are scattered through most of the genome, and can be stable enough to reconstruct genealogies spanning decades of the history of the NC4 lineage. The expression level of many duplicated genes is increased with dosage, but for others it appears that some form of dosage compensation occurs.
2008-04-21 | E-TABM-394 | biostudies-arrayexpress
Project description:Small RNAs play crucial roles in regulation of gene expression in many eukaryotes. Here, we report the cloning and characterization of 18-26 nt RNAs in the social amoeba Dictyostelium discoideum. This survey uncovered developmentally regulated microRNA candidates whose biogenesis, at least in one case, is dependent on a Dicer homolog, DrnB. Furthermore, we identified a large number of 21 nt RNAs originating from the DIRS-1 retrotransposon, clusters of which have been suggested to constitute centromeres. Small RNAs from another retrotransposon, Skipper, were significantly up-regulated in strains depleted of the second Dicer-like protein, DrnA, and a putative RNA-dependent RNA polymerase, RrpC. In contrast, the expression of DIRS-1 small RNAs was not altered in any of the analyzed strains. This suggests the presence of multiple RNAi pathways in D. discoideum. In addition, we isolated several small RNAs with antisense complementarity to mRNAs. Three of these mRNAs are developmentally regulated. Interestingly, all three corresponding genes express longer antisense RNAs from which the small RNAs may originate. In at least one case, the longer antisense RNA is complementary to the spliced but not the unspliced pre-mRNA, indicating synthesis by an RNA-dependent RNA polymerase. Keywords: cDNA library; small RNA sequencing The aim of this study was to investigate the small RNA (18-26 nt) profile of Dictyostelium discoideum during growth and development. For this reason, we cloned and sequenced pooled small RNAs from growing single cells and from two different multicellular stages (16 and 24 hours of development). cDNA libraries of 18-26 nt D. discoideum RNAs were constructed according to two different protocols (Lee, R.C. and Ambros, V. (2001) Science, 294; Lau, N.C. et al (2001) Science, 294). Briefly, total RNA was isolated from growing D. discoideum AX4 strain cells as well as from cells developed for 16 hours and 24 hours, and the fractions were subsequently pooled. After size fractionation and ligation of a 3’ linker, the RNA was divided into two fractions, one of which was directly ligated to a 5’ linker, thus selecting for small RNAs with 5’ monophosphates. Following RT-PCR, the PCR fragments were cloned and sequenced. The second fraction was subjected to reverse transcription directly after 3’ ligation. Apart from synthesizing a complementary DNA strand, the reverse transcriptase adds a few non-templated C residues at the 3’ end. These C:s were then hybridized to a DNA oligo with three 3’ G:s followed by RT-PCR, cloning and sequencing. This approach is insensitive of the nature of the 5’ end of the small RNA.
2007-10-16 | E-GEOD-8755 | biostudies-arrayexpress