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PROVIDER: PRJNA1288554 | ENA |
REPOSITORIES: ENA
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Project description:Botryllus schlosseri haplotypes hap1 and hap2 assemblies
| PRJNA1272845 | ENA
Project description:Botryllus schlosseri haplotypes hap2 assemblies
| PRJNA1273458 | ENA
Project description:Background: Gonad differentiation is an essential function for all sexually reproducing species, and many aspects of these developmental processes are highly conserved among the metazoa. The colonial ascidian, Botryllus schlosseri is a chordate model organism which offers two unique traits that can be utilized to characterize the genes underlying germline development: a colonial life history and variable fertility. These properties allow individual genotypes to be isolated at different stages of fertility and gene expression can be characterized comprehensively. Results: Here we characterized the transcriptome of both fertile and infertile colonies throughout blastogenesis (asexual development) using differential expression analysis. We identified genes (as few as 7 and as many as 647) regulating fertility in Botryllus at each stage of blastogenesis. Several of these genes appear to drive gonad maturation, as they are expressed by follicle cells surrounding both testis and oocyte precursors. Spatial and temporal expression of differentially expressed genes was analyzed by in situ hybridization, confirming expression in developing gonads. Conclusion: We have identified several genes expressed in developing and mature gonads in B. schlosseri. Analysis of genes upregulated in fertile animals suggests a high level of conservation of the mechanisms regulating fertility between basal chordates and vertebrates. mRNA profiles of seven infertile stages from infertile Botryllus schlosseri colonies (each in triplicates) and seven stages of fertile Botryllus schlosseri colonies (each in triplicates) using Illumina deep sequencing and analyzed for differential expression between each stage.
2015-01-12 | E-GEOD-62112 | biostudies-arrayexpress
Project description:Genome-wide association studies in multiple sclerosis (MS) identified a polymorphism (rs6897932) located in the coding region of the alpha chain of the cytokine receptor interleukin 7 receptor (IL7R) as a component that increases susceptibility to develop the disease. This single nucleotide polymorphism (SNP) affects the splicing of the primary transcript leading to genotype-defined transcript ratios encoding either a full length membrane spanning form or a soluble receptor chain. Genotyping at the IL7R locus reveals that the region can be described by four haplotypes. Interestingly, only one out of three haplotypes harbouring the associated SNP is positively associated with MS whereas the other two do not show association. The minor allele containing haplotype shows a reduced susceptibility to develop MS. We hypothesized that additional functional or phenotypic differences exist between individuals homozygous for haplotypes shown to have either positive, negative, or neutral effect, on susceptibility to develop MS. Gene expression profiles of CD4+ T cells from MS individuals before and after stimulation with IL7 were recorded. Haplotype-specific gene signatures were found indicating small alterations in IL7/IL7R signal processing/sensitivity through JAK/STAT and p38/MAPK14. We can not exclude that the obtained signatures result from differences within the CD4+ T cell compartment that, in fact, should be seen as a consequence of systemic haplotype-specific processing of homeostatic and proliferation signals transmitted through IL7/IL7R. Samples of CD4+ cells were obtained from 7 MS patients (homozygous for Hap1 (3), Hap2 (2), Hap3 (2)). CD4+ cells were collected from peripheral blood, frozen and stored in liquid nitrogen. All samples were thawed and CD4+ cells were purified by magnetic bead separation. Purity and viability of cells was analyzed by Fluorescence Activated Cell Sorter (FACS). Total cellular RNA were extracted with TRIzol reagent and analyzed with the Human Gene 1.0 ST Array (affymetrix). IL7R haplotypes and susceptibility to develop MS: Hap1 homozygous <-> Risk <-> positive effect on MS susceptibility Hap2 homozygous <-> Hap2 <-> neutral effect on MS susceptibility Hap3 homozygous <-> Prot <-> neutral effect on MS susceptibility [Note: Haplotype nomenclature subject to revision.]
2015-04-14 | E-GEOD-37584 | biostudies-arrayexpress
Project description:The study investigated the proteomic response of the colonial tunicate Botryllus schlosseri to acute copper exposure and subsequent recovery. DIA analysis was performed on Botryllus schlosseri colonies exposed to copper concentrations of 0 µg/L (control, C0), 300 µg/L (C3), and 900 µg/L (C4) for 24 hours (Exposure phase, E). To assess recovery (R), a subset of colonies from each condition was transferred to clean seawater for an additional 24 hours. Each condition included 11 biological replicates, collected by pooling ≥15 zooids per sample (including vascular network and ampullae).
2025-10-29 | PXD064899 | Pride
Project description:Highly polymorphic allorecognition systems have been characterized in numerous invertebrate species, and exhibit discriminatory capabilities reminiscent of vertebrate adaptive immunity. As these systems utilize germline encoded receptors, the mechanisms underlying allelic discrimination are unknown. The invertebrate chordate, Botryllus schlosseri, undergoes a natural transplantation reaction controlled by a highly polymorphic, polygenic locus (called the fuhc) with over 1,000 allelic haplotypes found worldwide. Two individuals are compatible if they share one or both fuhc alleles, and we had found that polymorphic discrimination is due to the integration of signals from two allorecognition receptors encoded within the fuhc locus, called fester and uncle fester. Here we show that these two receptors are members of an extended family consisting of >35 genes, now called the Fester family (FF), and co-expressed with members of another diverse gene family, the fester co-receptors (FcoR). Both FF and FcoR are Immunoglobulin superfamily members and each FcoR encodes conserved tyrosine signal transduction motifs, including ITIMs or hemITAMs. FF and FcoR are expressed and encoded as cognate pairs in two polymorphic haplotypes: one within the fuhc locus, and another on a separate chromosome, and remarkably, copy number variation between haplotypes is of gene pairs. Furthermore, two FcoR genes can swap ITIMs and hemITAMs by alternative splicing, suggesting that dynamic tuning of activating and inhibitory signaling is required for allelic discrimination. These results indicate that conserved signal processing mechanisms are the foundation of both allelic discrimination in Botryllus, and recurring convergent evolution of allorecognition receptors observed from invertebrates to mammals.
2025-10-06 | GSE295655 | GEO