Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
844
datasets available to search
ShareScore release 0.9.0
Dataset results
844 results for “germline”
Neuronal octopamine signaling regulates mating-induced germline stem cell increase in female Drosophila melanogaster
<p>Stem cells fuel the development and maintenance of tissues. Many studies have addressed how local signals from neighboring niche cells regulate stem cell identity and their proliferative potential. However, the regulation of stem cells by tissue-extrinsic signals in response to environmental cues remains poorly understood. Here we report that efferent octopaminergic neurons projecting to the ovary are essential for germline stem cell (GSC) increase in response to mating in female <i>Drosophila</i>. The neuronal activity of the octopaminergic neurons is required for mating-induced GSC increase as they relay the mating signal from Sex peptide receptor-positive cholinergic neurons. Octopamine and its receptor Oamb are also required for mating-induced GSC increase via intracellular Ca<sup>2+</sup> signaling. Moreover, we identified Matrix metalloproteinase-2 as a downstream component of the octopamine-Ca<sup>2+</sup> signaling to induce GSC increase. Our study provides a mechanism describing how neuronal system couples stem cell behavior to environmental cues through stem cell niche signaling.</p>
Towards genetic modification of plant-parasitic nematodes: Delivery of macromolecules to male germlines and expression of exogenous mRNA in second stage juveniles
<p>Plant-parasitic nematodes are a current and future threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics. Forward genetics is largely restricted to studies of natural variation in populations, and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate progress in plant-parasitic nematology, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic "tool kit" in plant-parasitic nematodes. We characterise the gonads of male <em>Heterodera schachtii</em> and Meloidogyne hapla in the context of spermatogenesis. We test and optimise various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of <em>H. schachtii</em> juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, and, taken together, will expedite the development of genetic modification protocols for sedentary endoparasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security.</p>
Germline and malignant melanoma sampled sequences containing point mutations
<p>Data files generated as part of a study into the influence of neighbouring bases on point mutation. The data are sampled from the Ensembl (http://www.ensembl.org) MySQL databases or COSMIC (http://cancer.sanger.ac.uk/cosmic) and processed using custom scripts that will be uploaded separately and associated with this submission via gthe related identifier.</p>
Quartet DNA benchmark sets for germline small variants and structural variants
Open the record for dataset details and reuse information.
Mutation, selection, and the prevalence of the C. elegans heat-sensitive mortal germline phenotype
<p><em>C. elegans</em> strains with the heat-sensitive mortal germline (Mrt) phenotype become progressively sterile over the course of a few tens of generations when maintained at temperatures near the upper range of <em>C. elegans'</em> tolerance. Mrt is transgenerationally-heritable, and proximately under epigenetic control. Previous studies have suggested that Mrt presents a relatively large mutational target, and that Mrt is not uncommon in natural populations of <em>C. elegans</em>. The Mrt phenotype is not monolithic. Some strains exhibit a strong Mrt phenotype, in which individuals invariably become sterile over a few generations, whereas other strains show a weaker (less penetrant) phenotype in which the onset of sterility is slower and more stochastic. We present results in which we (1) quantify the rate of mutation to the Mrt phenotype, and (2) quantify the frequency of Mrt in a collection of 95 wild isolates. Over the course of ~16,000 meioses, we detected one mutation to a strong Mrt phenotype, resulting in a point estimate of the mutation rate U<em><sub>Mrt</sub></em>≈ 6 10<sup>-5</sup>/genome/generation. We detected no mutations to a weak Mrt phenotype. 6/95 wild isolates have a strong Mrt phenotype, and although quantification of the weak Mrt phenotype is inexact, the weak Mrt phenotype is not rare in nature. We estimate a strength of selection against mutations conferring the strong Mrt phenotype ≈0.1%, similar to selection against mutations affecting competitive fitness. The appreciable frequency of weak Mrt variants in nature combined with the low mutation rate suggests that Mrt may be maintained by balancing selection.</p>
Immune Evasion and Epithelial-to-Mesenchymal Transition in Fallopian Tube as an Early Event for Ovarian Cancer Development in Women with Germline BRCA1 Mutation
<p>The single cell RNA-seq and TCR-seq data of BRCA1 mutation carriers and normal controls</p>
Open Germline Receptor Database (OGRDB) Archive
<p>Periodic archive of the OGRDB database</p>
Germline Immunomodulatory Expression Quantitative Trait Loci (ieQTLs) Associated with Immune-Related Toxicity from Checkpoint Inhibition
<p>Robert Ferguson<sup>1,2,3*</sup>, Vylyny Chat<sup>1,2,3*</sup>, Leah Morales<sup>1,2,3</sup>, Danny Simpson<sup>1,2,3</sup>, Kelsey Monson<sup>1,2,3</sup>, Elisheva Cohen<sup>1,2,3</sup>,Sarah Zusin<sup>1,2,3</sup>, Gabriele Madonna<sup>4</sup>, Mariaelena Capone<sup>4</sup>, Ester Simeone<sup>4</sup>, Anna Pavlick<sup>5</sup>, Jason Luke<sup>6,7</sup>, Thomas F Gajewski<sup>8,9,10</sup>, Iman Osman<sup>1,3,11,12</sup>, Paolo Antonio Ascierto<sup>4</sup>, Jeffrey Weber<sup>1,3,11</sup>, Tomas Kirchhoff<sup>1,2,3</sup></p> <p>1Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA<br> 2Departments of Population Health and Environmental Medicine, New York University- Grossman School of Medicine, New York, NY, USA<br> 3The Interdisciplinary Melanoma Cooperative Group, New York University-Grossman School of Medicine, New York, NY, USA<br> 4Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy<br> 5Division of Hematology & Medical Oncology, the Cutaneous Oncology Program, Weill Cornell Medicine and New York-Presbyterian, New York, USA<br> 6Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA.<br> 7UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA.<br> 8Department of Pathology, University of Chicago, Chicago, IL, USA.</p> <p>9Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA.<br> 10Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA.<br> 11Department of Medicine, New York University-Grossman School of Medicine, New York, NY, USA<br> 12Ronald O. Perelman Department of Dermatology, New York University-Grossman School of Medicine, New York, NY, USA</p> <p>*These authors contributed equally to the work</p> <p>Corresponding author: Tomas Kirchhoff, PhD</p> <p><strong>ABSTRACT</strong><br> <strong>Background:</strong> Immune-checkpoint inhibition (ICI) has improved clinical outcomes for metastatic melanoma patients, however, 65-80% of patients treated with ICI experience immune-related adverse events (irAEs). Given the plausible link of irAEs with underlying host immunity, we explored if germline genetic variants controlling the expression of 42 immunomodulatory genes<br> were associated with the risk of irAEs in melanoma patients treated with the single-agent anti- CTLA-4 antibody ipilimumab (IPI).<br> <strong>Methods:</strong> We identified 42 immunomodulatory expression quantitative trait loci (ieQTLs) most significantly associated with the expression of 382 immune-related genes. These germline variants were genotyped in IPI-treated melanoma patients, collected as part of a multiinstitutional collaboration. We tested the association of ieQTLs with irAEs in a discovery cohort of 95 patients followed by validation in an additional 97 patients.<br> Results: We found that the alternate allele of rs7036417, a variant linked to increased expression of SYK, was strongly associated with an increased risk of grade 3-4 toxicity (OR= 7.46; 95% CI=2.65-21.03; p=1.43E-04). This variant was not associated with response (OR= 0.90; 95% CI=0.37-2.21; p=0.82).<br> Conclusion: We report that rs7036417 associates with increased risk of severe irAEs, independent of IPI efficacy. SYK plays an important role in B-cell/T-cell expansion and increased pSYK has been reported in patients with autoimmune disease. The association between rs7036417 and IPI irAEs in our data suggests a role of SYK over-expression in irAE development. These findings support the hypothesis that inherited variation in immune-related pathways modulate ICI toxicity and suggest SYK as a possible future target for therapies to reduce irAEs.</p> <p> </p> <p><strong>Keywords:</strong> irAEs; germline variants; immune checkpoint inhibition; melanoma</p> <p><strong>Funding:</strong> This research was funded by the Italian Ministry of Health (IT-MOH) through “Ricerca Corrente”, grants number M2/2 and L2-1.</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Germline stem progenitors and oocyte production in the Honeybee Queen Ovary
<p>Raw figures for the paper “Germline stem progenitors and oocyte production in the Honeybee Queen Ovary”.</p> <p> Georgia Cullen, Joshua B. Gilligan, Joseph G. Guhlin and Peter K. Dearden.</p>
Triple Negative Breast Cancer and Germline Hereditary Breast and Ovarian Cancer Mutation Carrier Registry
ClinicalTrials.gov study NCT02302742. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Cutaneous Mastocytosis in Children: Analysis of Somatic and Germline Mutations
ClinicalTrials.gov study NCT02761473. IPD Sharing: NO. Countries: 1. Publications: 4.
Platinum and Polyadenosine 5'Diphosphoribose Polymerisation Inhibitor for Neoadjuvant Treatment of Triple Negative Breast Cancer and/or Germline BRCA Positive Breast Cancer
ClinicalTrials.gov study NCT03150576. IPD Sharing: YES. Countries: 1. Publications: 3.
Multigene Germline Panel Testing in Gastric Cancer Patients in Portugal
ClinicalTrials.gov study NCT07387237. IPD Sharing: YES. Countries: 1. Publications: 0.
Technology-Enhanced Acceleration of Germline Evaluation for Therapy, TARGET Study
ClinicalTrials.gov study NCT04447703. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Circulating Tumor DNA and BRCA Reversion Mutation in Advanced or Recurrent Ovarian Cancer Patients With Germline Mutation.
ClinicalTrials.gov study NCT05458973. IPD Sharing: NO. Countries: 1. Publications: 1.
Parental Irradiation of Ukrainian Cleanup Workers and Evacuees and Germline Mutations in Their Offspring (Trio Study)
ClinicalTrials.gov study NCT02566161. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Promoting Men's Adherence to BRCA1/2 Germline Genetic Testing
ClinicalTrials.gov study NCT04683068. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Integrative Sequencing In Germline and Hereditary Tumours
ClinicalTrials.gov study NCT03857594. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Risk-reducing Strategies, Including Fimbriectomy, in Women With a Germline Mutation Predisposing to Ovarian or Pelvic Cancer
ClinicalTrials.gov study NCT06726330. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Natural History Study of Individuals With Autism and Germline Heterozygous PTEN Mutations
ClinicalTrials.gov study NCT02461446. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
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.