Sponge development
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina Genome Analyzer II
ORGANISM(S): Sycon ciliatum
SUBMITTER: Marcin Adamski
PROVIDER: E-MTAB-2890 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:In order to compare sponge and eumetazoan (higher animal) body plans, we identified and studied expression of a broad range of eumetazoan developmental regulatory genes in Sycon ciliatum (Calcispongiae). In this species, embryonic development is semi-synchronous within a population, synchronous within individuals, and oocytes and embryos occupy a significant fraction of the volume of the sponges during the reproductive period. RNASeq libraries representing non-reproductive (somatic) tissue slices along the body axis, as well as oocytes, embryos and free swimming larvae were generated from material obtained by sampling throughout the life cycle.
2014-05-01 | E-MTAB-2431 | biostudies-arrayexpress
Project description:In order to compare sponge and eumetazoan (higher animal) body plans, we identified and studied expression of a broad range of eumetazoan developmental regulatory genes in Sycon ciliatum (Calcispongiae). In this species, embryonic development is semi-synchronous within a population, synchronous within individuals, and oocytes and embryos occupy a significant fraction of the volume of the sponges during the reproductive period. RNASeq libraries representing non-reproductive (somatic) tissue slices along the body axis, as well as oocytes, embryos and free swimming larvae were generated from material obtained by sampling throughout the life cycle.
2014-05-01 | E-MTAB-2430 | biostudies-arrayexpress
Project description:The 987 probes (Japanese flounder conserved miRNAs and candidates, fish conserved miRNAs, and contro) were hybridized with two stages during Japanese flounder metamorphosis by miRNA microarray. We validated 92 miRNAs using miRNA microarray in the 17 dph and 29 dph of Japanese flounder development, and obtained 66 differertially expressed miRNAs by comparison miRNA expression patterns of the two stages. These results indicate that miRNAs might play key roles in regulating gene expression during Japanese flounder metamorphosis. Using miRNA microarray, the flounder conserved miRNAs and candidates were identified, and 92 conserved miRNAs were detected in the 17 dph and 29 dph during metamorphosis. Meanwhile, 66 conserved miRNAs were differertially expressed by comparison miRNA expression patterns of the two stages. We further identified flounder miRNAs during metamorphosis.
2013-03-10 | E-GEOD-27986 | biostudies-arrayexpress
Project description:Molting is an essential biological process occurring characteristic times throughout the life cycle of holometabolous insects. However, it is not clear how insects determine whether the direction of molting is to remain status quo or to initiate metamorphosis. Here, we used liquid chromatography-mass spectrometry to identify the molecules involved in larval and metamorphic molting, and compare the differentially expressed proteins (DEPs) in the two processes, to explore the functional factors that determine the direction of molts. There were 322 and 1140 DEPs identified in larval and metamorphic molting process, respectively. Bioinformatics analyses show that the amino sugar pathway was up-regulated in both processes. The up-regulated protease contributed to the metamorphosis. In addition, several proteins with different expression patterns in larval-larval and larval-pupal transitions, including Endochitinase, GRIM-19 (Genes associated with retinoid-IFN-induced mortality-19), IDE (Insulin-degrading enzyme), Sorcin (Soluble resistance related calcium binding protein), OBP (Odorant-binding protein-2 precursor), TRAP1(Tumor necrosis factor receptor associated protein-1), etc., were further identified by parallel reaction monitoring, which may play diverse functions in the determination of molting properties. These results provide a proteomic insight into molecules involved in larval and metamorphic molts, and will likely improve the current understanding of determination of direction of molts.
2020-10-30 | PXD020414 | Pride
Project description:Many known miRNAs in fish come from zebrafish and fugu whose genome sequence data are available. The Japanese flounder undergoes typical metamorphosis which is characterized by major morphological, functional, and behavioral changes during growth due to this metamorphosis from larva to juvenile. Metamorphosis is a biological process by which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's body structure through cell growth and differentiation. Here, the high-throughput sequencing was adopted to identify the miRNAs during metamorphosis in the Japanese flounder. We found abundant microRNAs during metamorphosis in the Japanese flounder. Small RNAs were sequenced from metamorphosis stages of Japanese flounder
2010-12-23 | E-GEOD-25995 | biostudies-arrayexpress
Project description:Larval settlement and metamorphosis is a vital transition period for marine invertebrates and can have far-reaching effects on the ecology and evolution of a species. To explore the molecular mechanisms of this critical process in a non-model organism, the tropical abalone Haliotis asinina, we employed cDNA microarray methods. By comparing gene expression profiles through mid to late larval development and metamorphosis, we identified 144 genes as likely candidates for a role in competence and/or metamorphosis. Gene characterization showed that ~60% of these were significantly similar to previously described genes from other taxa, while ~40% had no significant similarities to any known genes. A high 49.3% of genes were gastropod- or abalone-specific, but none appear to be Lophotrochozoan-specific, despite the fact that metamorphosis is thought to have had a separate origin in this group. Based on temporal expression profiles, the differentially expressed larval and postlarval genes can be clustered into 5 categories that reveal there are strikingly different transcriptional patterns occurring during this phase of development. Some classes of gene activation are contingent upon exogenous cues and correlate with the initiation of settlement and metamorphosis. Importantly, there is also extensive gene activity associated with the endogenous attainment of competence, which occurs prior to, and independent of, the exogenous induction of settlement. Our results show that as the haliotid veliger larva matures, it requires the coordinated regulation of temporally different batteries of genes involved in a wide range of physiological and developmental processes associated with colonisation of the benthos. Although the signalling pathways operating at metamorphosis may be conserved across the animal kingdom, it appears they are regulating the expression of novel genes specific to abalone, gastropods and molluscs during H. asinina metamorphosis. Keywords: timecourse; metamorphosis; marine ecology Each microarray slide contained a different combination of 2 of the 9 developmental stages used in the experiment (66 hpf, 78 hpf, 90 hpf, 108 hpf, 120 hpf, 144 hpf, 12 hpi, 24 hpi, 48 hpi). Each developmental stage was subjected to 4 hybridisations â amounting to 4 technical replicates per stage - in a loop design (Churchill 2002; Oleksiak et al. 2002). This design led to raw data consisting of 72 measurements - 9 stages with 8 replicates (including 2 replicates per chip) - for each of 5541 spots.
2010-05-19 | E-GEOD-13039 | biostudies-arrayexpress
Project description:We report a comprehensive DNA accessibility profile of the Demosponge species Amphimedon queenslandica using Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) through six embryonic developmental stages, a larval stage and adult stage. We assessed the dynamics of chromatin accessibility and identified 40,218 consensus peaks, 4,751 of them were differentially accessible in at least one developmental stage. Cis-regulatory elements were more dynamically regulated while proximal elements were more likely to be constitutively active. Furthermore, we identify a shift towards repressive chromatin in mid and late developmental stages which coincide with the increase in expression of genes of Metazoan origin. Finally, we show that cis-regulatory regions are differentially enriched in different Transcription Factor binding sites (TFBS) which demarcate three main stages of development and importantly, they are predictive of cis-regulatory regions in other animal species but not in Capsaspora owczarzaki, a close relative of animals.
2021-10-10 | E-MTAB-10203 | biostudies-arrayexpress
Project description:African clawed frog Xenopus sp. is used extensively for developmental biology and toxicology research. Amid concerns of environmental pollutants disrupting endocrine systems and causing altered reproductive development in wildlife, eco-toxicology research has led to a focus on linking molecular initiating events to population-level effects. As such, efforts to better understand reproductive development at the molecular level in these model species are warranted. To that end, transcriptomes were characterized in differentiating Xenopus tropicalis gonad tissues at Nieuwkoop and Faber (NF) stage 58 (pro-metamorphosis), NF66 (completion of metamorphosis), one week post-metamorphosis (1WPM), and two weeks post-metamorphosis (2WPM). Differential expression analysis between tissue types at each developmental stage revealed a substantial divergence of ovary and testis transcriptomes starting between NF58 and NF66; transcriptomes continued to diverge through 2WPM. Generally, testis-enriched transcripts were expressed at relatively constant levels, while ovary-enriched transcripts were up-regulated within this developmental period. Functional analyses of differentially expressed transcripts allowed linkages to be made between their putative human orthologues and specific cellular processes associated with differentiating gonad tissues. In ovary tissue, genetic programs direct germ cells through meiosis to the diplotene stage when maternal mRNAs are transcribed and trafficked to oocytes for translation following fertilization. In the testis, gene expression is consistent with connective tissue development, tubule formation, and germ cell support (Leydig and Sertoli cells). This dataset exhibited remarkable consistency with transcript profiles previously described in gonad tissues across species, and emphasizes the universal importance of certain transcripts for germ cell development and preparation of these tissues for reproduction. Four developmental time-points were considered for global expression analysis: NF58 (pro-metamorphosis), NF66 (completion of metamorphosis), one week post-metamorphosis (1WPM), and two weeks post-metamorphosis (2WPM). Gonad tissues were time-matched and stage-matched, so collection occurred on a single day for each developmental time-point and all animals used were from the same spawn. For the 1WPM and 2WPM time-points, all animals reached NF66 on the same day and were separated from the rest of the spawn until sample collection one and two weeks later respectively. On the day of tissue collection, animals were developmentally staged (Nieuwkoop and Faber, 1994) and euthanized by submersion in a lethal concentration of tricane methanesulfonate ([MS-222], Argent Chemical Laboratories, Redmond, WA, USA) buffered with sodium bicarbonate. Gonad tissues were then excised independently of any other tissues (i.e. “pure” gonad tissue) and transferred to a separate vial for each individual, homogenized in lysis buffer from an RNeasy micro kit (Qiagen Inc., Valencia, CA, USA), and immediately frozen on dry ice until samples could be moved to -80oC storage. Tail or toe tissue was also collected from each individual for genetic sex determination using methods previously described by Olmstead et al. (2010). Once genetic sex was determined for each individual, testes and ovaries were randomly assigned to pools of four individuals (eight gonads per pool) to make a total of five pools of testis tissue and five pools of ovary tissue at each developmental time-point, with the exception of NF58 which had four pools of testis tissue and four pools of ovary tissue (38 total sample pools).
2014-07-31 | E-GEOD-58612 | biostudies-arrayexpress
Project description:We analyzed the proteomes of competent Rapna venosa larvae and post-larvae, resulting in the identification of 5,312 proteins, including 470 that were down-regulated and 668 that were up-regulated after metamorphosis. The differentially expressed proteins reflected multiple processes involved in metamorphosis, including cytoskeleton and cell adhesion, ingestion and digestion, stress response and immunity, as well as specific tissue development. Our data improve understanding of the physiological traits controlling R. venosa metamorphosis and provide a solid basis for further study.
2018-10-26 | PXD004119 | Pride
Project description:Induction of Xenopus laevis larvae metamorphosis is dependent on exposure to TH. Metamorphosis involves the regression, growth or remodeling of almost all the tissues in the animals body. Metamorphosis in frogs is induced by thyroid hormone. Each organ system has a unique morphological and genetic program that it follows while undergoing metamorphosis involving both the upregulation and downregulation of genes. In this array we examined the change in gene expression in the tail of larvae undergoing precocious metamorphosis following induction with thyroid hormone. Whole stage 54 xenopus larvae were exposed to either vehicle for 48 hours or 20 nM T3 for 6 or 48 hours. Total RNA was then purified from tail tissue and the samples were examined by hybridization to the Affymetrix Xenopus array. Developmental stage 51-54 Xenopus larvae were selected because these stages do not express high levels of endogenous T3 but are still capable of morphologically responding to exposure.
2010-07-30 | E-GEOD-22643 | biostudies-arrayexpress