High-resolution genome-wide transcriptomics analysis of O. dioica development
Ontology highlight
ABSTRACT:
ORGANISM(S): Oikopleura dioica
PROVIDER: GSE39568 | GEO | 2012/07/24
SECONDARY ACCESSION(S): PRJNA171145
REPOSITORIES: GEO
Similar Datasets
Project description:The developmental transcriptomics of every significant developmental stage of O. dioica at ultra-high resolution. 18 samples were included, each in technical triplicate (and one with 4 replicates). These samples included 12 developmental time-point providing high-resolution interrogation of the complete animal life cycle. A further 3 samples specifically interrogated adult ovary, testis and somatic tissues. Finally, 3 samples were included that covered animal transcriptomics response under restrictive conditions that induce developmental growth arrest.
2012-07-23 | E-GEOD-39568 | biostudies-arrayexpress
Project description:Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in the marine chordate Oikopleura dioica and find evidence for proposed functions of SL-trans-splicing. A recent hypothesis postulates that operons facilitate recovery from growth arrested states in metazoans. We examined the expression dynamics of operons across the life-cycle of the animal and during growth arrest recovery. We show that operons do not facilitate recovery from growth arrest in O. dioica. We find that operons are enriched in the germline and that trans-spliced transcripts are predominantly maternal., Interestingly, there is a TOP-like motif in the SL sequence, and trans-splicing in TOP mRNAs, indicating that trans-spliced mRNAs are targets for nutrient-dependent translational control in O. dioica. Whole animals were sampled from a growth arrested state as well as three time points after release from growth arrest: 0.5 hrs; 1.5 hrs and 4 hrs. Two biological replicates were performed for each time point and each of these was divided into three technical replicates.
2015-01-26 | E-GEOD-50848 | biostudies-arrayexpress
Project description:Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in the marine chordate Oikopleura dioica and find evidence for proposed functions of SL-trans-splicing. A recent hypothesis postulates that operons facilitate recovery from growth arrested states in metazoans. We examined the expression dynamics of operons across the life-cycle of the animal and during growth arrest recovery. We show that operons do not facilitate recovery from growth arrest in O. dioica. We find that operons are enriched in the germline and that trans-spliced transcripts are predominantly maternal., Interestingly, there is a TOP-like motif in the SL sequence, and trans-splicing in TOP mRNAs, indicating that trans-spliced mRNAs are targets for nutrient-dependent translational control in O. dioica.
2015-01-26 | GSE50848 | GEO
Project description:High-resolution genome-wide transcriptomics analysis of O. dioica development
| PRJNA171145 | ENA
Project description:The selection and activity of transcription start sites (TSSs) are central to gene regulation and depend on sequence and chromatin features within a core promoter region. We present, at single-bp resolution, the TSS landscape of Oikopleura dioica, a marine chordate in the sister group to vertebrates and relate dynamics of promoter usage, and their architectures, across its life cycle, to chromatin features. TSS selection grammars include a genome-wide shift during spermatogenesis to promoters with a novel, position-specific, core promoter element, present in >70% of male-specific promoters. Differential promoter usage in spermatogenesis includes the activation of cryptic internal promoters within polycistronic operons, alternative TSS selection within promoters of genes expressed in earlier development and the exclusion of trans-splice sites. In contrast, maternal promoters, which are active in endocycling nurse nuclei in O. dioica, lack position-specific motifs, have dispersed TSS usage, ordered nucleosomes around the TSS and typical histone modifications associated with broad promoters. Furthermore, our results indicate that the cell cycle regulator, E2F1, acts as a master regulator of these maternally expressed genes. Zygotic promoters are also predominantly broad and the vertebrate maternal to zygotic switch in mode of TSS-selection is absent. DNA methylation in gene bodies is an ancient property of eukaryotic genomes and is thought to repress alternative TSSs. We report a strong association between gene body DNA methylation, H3K4me3-depletion and TATA-dependent sharp promoters in O. dioica. Core promoter features may therefore determine the subset of gene bodies that are methylated in this invertebrate genome.
2018-02-05 | GSE78794 | GEO
Project description:High-resolution genome-wide transcriptomics analysis of O. dioica during recovery from growth arrest
| PRJNA219163 | ENA
Project description:Ultra high resolution breakpoint mapping using custom oligonucleotide arrays and array painting The two derivative chromosomes from 4 patients with balanced translocations were flow sorted, differentially labelled and hybridised to custom oligonucleotide arrays designed to cover the potential breakpoint region at high resolution. Single hybridisations with no replicates.
2010-07-01 | E-GEOD-4297 | biostudies-arrayexpress
Project description:Ultra high resolution breakpoint mapping using custom oligonucleotide arrays and array painting Keywords: Breakpoint mapping
2006-11-01 | GSE4297 | GEO
Project description:High-resolution single worm transcriptomics in Pritionchus pacificus
| PRJEB42613 | ENA