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130 results for “developmental programming”
Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
<p>With its nuclear dualism, the ciliate <em>Paramecium</em> constitutes an original model to study how host genomes cope with transposable elements (TEs). <em>P. tetraurelia</em> harbors two germline micronuclei (MIC) and a polyploid somatic macronucleus (MAC) that develops from the MIC at each sexual cycle. Throughout evolution, the MIC genome has been continuously colonized by TEs and related sequences that are removed from the somatic genome during MAC development. Whereas TE elimination is generally imprecise, excision of ~45000 TE-derived Internal Eliminated Sequences (IESs) is precise, allowing for functional gene assembly. Programmed DNA elimination is concomitant with genome amplification. It is guided by non-coding RNAs and repressive chromatin marks. A subset of IESs are excised independently of this epigenetic control, raising the question of how they are targeted for elimination. To gain insight into the determinants of IES excision, we determined the developmental timing of DNA elimination genome-wide by combining fluorescence-assisted nuclear sorting with next-generation sequencing. Essentially all IESs are excised within one endoduplication round only (32C to 64C), while TEs are eliminated at a later stage. We show that time, rather than replication, controls the progression of DNA elimination. Further analyses defined four IES classes according to excision timing and revealed that the earliest excised IESs tend to be independent of epigenetic factors, display strong sequence signals at their ends and originate from the most ancient integration events. We conclude that old IESs have been optimized during evolution for early and accurate excision, by acquiring stronger sequence determinants and escaping epigenetic control.</p>
Data for: Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence
<p><span>In cereal crops such as barley (<em>Hordeum vulgare</em> L.), pre-anthesis tip degeneration (PTD) starts with growth arrest of the inflorescence meristem dome, followed basipetally by the degeneration of floral primordia and the central axis. Due to its quantitative nature and environmental sensitivity, inflorescence PTD constitutes a complex, multilayered trait affecting final grain number. This trait was studied by microscopic dissection of immature inflorescence meristems under standardized growth conditions. We combined spatiotemporal metabolomic, transcriptomic, and genetic approaches to elucidate the mechanism of barley inflorescence PTD in two- and six-rowed barley cultivars 'Bowman' and 'Morex,' respectively. Metabolome profiling includes hormones and primary metabolites such as sugars, TCA intermediates, and amino acids by dividing spike meristems into dying apical and viable central and basal parts at four developmental stages during the spike growth phase. </span>Similarly, RNA sequencing was performed for three developmental stages in both genotypes. RNA sequencing data analyses were performed to identify differentially expressed and tissue-specific transcripts. Further, PTD-associated hub genes were identified by weighted gene coexpression network analysis. Based on transcriptome analyses, we identified an important modulator of inflorescence PTD and functionally validated it using Cas9-mediated mutagenesis and gene-based associated study using a diverse panel of barley accessions. </p>
Data for: Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence
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Transcriptional patterns of sexual dimorphism and in host developmental programs in the model parasitic nematode Heligmosomoides bakeri
<p><strong>Background</strong></p> <p><em>Heligmosomoides bakeri </em>(often mistaken for <em>Heligmosomoides</em> <em>polygyrus</em>) is a promising model for parasitic nematodes with the key advantage of being amenable to study and manipulation within a controlled laboratory environment. While draft genome sequences are available for this worm, which allow for comparative genomic analyses between nematodes, there is a notable lack of information on its gene expression.</p> <p><strong>Methods </strong></p> <p>We generated biologically replicated RNA-seq datasets from samples taken throughout the parasitic life of <em>H. bakeri</em>. RNA from tissue-dwelling and lumen-dwelling worms, collected under a dissection microscope, was sequenced on an Illumina platform. <strong> </strong></p> <p><strong>Results</strong></p> <p>We find extensive transcriptional sexual dimorphism throughout the fourth larval and adult stages of this parasite and identify alternative splicing, glycosylation, and ubiquitination as particularly important processes for establishing and/or maintaining sex-specific gene expression in this species. We find sex-linked differences in transcription related to aging and oxidative and osmotic stress responses. We observe a starvation-like signature among transcripts whose expression is consistently upregulated in males, which may reflect a higher energy expenditure by male worms. We detect evidence of increased importance for anaerobic respiration among the adult worms, which coincides with the parasite's migration into the physiologically hypoxic environment of the intestinal lumen. Furthermore, we hypothesize that oxygen concentration may be an important driver of the worms encysting in the intestinal mucosa as larvae, which not only fully exposes the worms to their host's immune system but also shapes many of the interactions between the host and parasite. We find stage- and sex-specific variation in the expression of immunomodulatory genes and in anthelmintic targets. <strong> </strong></p> <p><strong>Conclusions</strong></p> <p>We examine how different the male and female worms are at the molecular level and describe major developmental events that occur in the worm, which extend our understanding of the interactions between this parasite and its host. In addition to generating new hypotheses for follow-up experiments into the worm's behavior, physiology, and metabolism, our datasets enable future more in-depth comparisons between nematodes to better define the utility of <em>H. bakeri</em> as a model for parasitic nematodes in general. </p>
Early Intervention in Preterm Infants: Short and Long Term Developmental Outcome After a Parental Training Program
ClinicalTrials.gov study NCT02983513. IPD Sharing: NO. Countries: 1. Publications: 8.
Transcriptional patterns of sexual dimorphism and in host developmental programs in the model parasitic nematode Heligmosomoides bakeri
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Data from: Adaptive maternal behavioral plasticity and developmental programming mitigate the transgenerational effects of temperature in dung beetles
Phenotypic plasticity allows organisms to cope with rapid environmental change. Yet exactly when during ontogeny plastic responses are elicited, whether plastic responses produced in one generation influence phenotypic variation and fitness in subsequent generations, and the role of plasticity in shaping population divergences, remains overall poorly understood. Here, we use the dung beetle <i>Onthophagus taurus</i> to assess plastic responses to temperature at several life stages bridging three generations and compare these responses across three recently diverged populations. We find that beetles reared at hotter temperatures grow less than those reared at mild temperatures, and that this attenuated growth has transgenerational consequences by reducing offspring size and survival in subsequent generations. However, we also find evidence that plasticity may mitigate these consequences in two ways: (i) mothers modify the temperature of their offspring's developmental environment via behavioral plasticity and (ii) in one population, offspring exhibit accelerated growth when exposed to hot temperatures during very early development ("developmental programming"). Lastly, our study reveals that offspring responses to temperature diverged among populations in fewer than 100 generations, possibly in response to range-specific changes in climatic or social conditions.
Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation
<p>Raw microscopy images underlying the publication "Single-cell and spatial transcriptomics reveal aberrant lymphoid developmental programs driving granuloma formation"</p>
Application of the Best Evidence of Neonatal Individualized Developmental Care Assessment Program (NIDCAP) in Very Low Birth Weight Infant (VLBWI)
ClinicalTrials.gov study NCT05166720. IPD Sharing: Not stated. Countries: 1. Publications: 1.
An Evaluation of a Developmentally-Based Parent Training Program for Children With Autism
ClinicalTrials.gov study NCT01400269. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Implementation of a Teacher Classroom Program to Support Preschool Children With Autism or Developmental Problems
ClinicalTrials.gov study NCT06790199. IPD Sharing: NO. Countries: 1. Publications: 2.
Efficacy Trial of the Kids in Transition to School (KITS) Program for Children With Developmental Disabilities and Behavioral Problems
ClinicalTrials.gov study NCT01593189. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Adaptive maternal behavioral plasticity and developmental programming mitigate the transgenerational effects of temperature in dung beetles
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Effect of a Psychoeducational-Developmental Support Program on Adolescents' Relative Deprivation, Distress Levels, Peer Relations and Basic Psychological Needs
ClinicalTrials.gov study NCT07291349. IPD Sharing: NO. Countries: 1. Publications: 0.
A targetable developmental program co-regulates angiogenesis and immune evasion.
GEO Series GSE312368. Homo sapiens; Mus musculus. 77 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing.
A developmentally programmed splicing failure attenuates the DNA damage response during mammalian zygotic genome activation
GEO Series GSE163205. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts [CLIP-Seq]
GEO Series GSE45828. Mus musculus. 2 samples. Type: Other.
Developmental programs in childhood neuroblastoma [scRNA-seq SK-N-AS]
GEO Series GSE163430. Homo sapiens. 16 samples. Type: Expression profiling by high throughput sequencing.
Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila
GEO Series GSE245033. Drosophila melanogaster. 24 samples. Type: Other.
Developmental and housekeeping transcriptional programs in Drosophila require distinct chromatin remodelers (PROseq)
GEO Series GSE184183. Drosophila melanogaster. 26 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.