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”
Raw data for Development of Germline Progenitors in Larval Queen Honeybee ovaries
<p>This repository contains raw files for images relating to a publication of honeybee ovary development. That work is Cullen, Delargy and Dearden 2024, <strong><span>Development of Germline Progenitors in Larval Queen Honeybee ovaries. </span></strong><span>The data is organised in folders relate to each figure, and is in .oir format, a raw data format produced by Olympus confocal systems. This data file format is able to be read by FIJI.</span></p>
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>
Germline CpG methylation signatures in the human population inferred from genetic polymorphism
<p>This repository contains data released accompanying the manuscript "Germline CpG methylation signatures in the human population inferred from genetic polymorphism". </p>
Data from: Coevolution of longevity and female germline maintenance
<p>An often-overlooked aspect of life-history optimization is the allocation of resources to protect the germline and secure safe transmission of genetic information. While failure to do so renders significant fitness consequences in future generations, germline maintenance comes with substantial costs. Thus, germline allocation should trade-off with other life history decisions and be optimized in accordance with an organism's reproductive schedule. Here we tested this hypothesis by studying germline maintenance in lines of seed beetle, selected for early (E) or late (L) reproduction for 350 and 240 generations, respectively. Female animals provide maintenance and screening of male gametes in their reproductive tract and oocytes. Here, we revealed the ability of young and aged E and L-females to provide this form of germline maintenance by mating them to males with ejaculates with artificially elevated levels of protein and DNA damage. We find that germline maintenance in E-females peaks at young age and then declines, while the opposite is true for L-females, in accordance with the age of reproduction in respective regime. These findings identify the central role of allocation to secure germline integrity in life history evolution and highlight how females can play a crucial role in mitigating effects of male germline decisions on mutation rate and offspring quality.</p>
Systematic analysis of disease-linked rare germline variants reveals new classes of cancer predisposing genes
<ul> <li>GEMs_Liver-HCC: 312 cancer patient-specific genome-scale metabolic models (GEMs) for Liver-HCC reconstructed using the RNA-seq data from PCAWG-TCGA Liver-HCC samples and generic human GEM 'Recon 2M.2'</li> <li>GEMs_Lung-SCC: 493 cancer patient-specific GEMs for Lung-SCC reconstructed using the RNA-Seq data from PCAWG-TCGA Lung-SCC samples and generic human GEM 'Recon 2M.2'</li> </ul> <p>All the patient-specific GEMs were generated using a previously developed method (i.e., tINIT algorithm with a rank-based weight function), which is available at <a href="https://bitbucket.org/kaistmbel/recon-manager">https://bitbucket.org/kaistmbel/recon-manager</a>.</p>
TCR-MHC Germline Interaction Scores Generated Using AIMS
<p>These data were generated using the AIMS interaction scoring function as outlined in the manuscript "A Systematic Characterization of Germline-Encoded Contacts Identifies the Source of Bias in TCR-MHC Interactions". They accompany the AIMS version 0.7 software available on GitHub: https://github.com/ctboughter/AIMS . These files are meant to be loaded into the mhc_germline_analysis.ipynb file, but are too large to be included on the GitHub page itself.</p>
Data accompanying "HSP70 inhibits CHIP E3 ligase activity to maintain germline function in Caenorhabditis elegans" article.
<p>This work was funded by the National Science Centre, Poland (grant PRELUDIUM number 2021/41/N/NZ1/03086) (to P.T.) and by the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation) under Germany’s Excellence Strategy – EXC 2030 – 390661388 and – FOR 5504 – project number 496650118 (to T.H.). M.T.P. received support by the Cologne Graduate School of Aging Research. N.A.S., A.S., K.J., and M.N. were supported by the International Institute of Molecular and Cell Biology in Warsaw.</p>
Alpelisib Plus Olaparib in Platinum-resistant/Refractory, High-grade Serous Ovarian Cancer, With no Germline BRCA Mutation Detected
ClinicalTrials.gov study NCT04729387. IPD Sharing: YES. Countries: 26. Publications: 1.
Data from: Coevolution of longevity and female germline maintenance
Open the record for dataset details and reuse information.
Data from: Highly efficient generation of germline mutations using CRISPR/Cas9 in the speckled wood butterfly Pararge aegeria
Open the record for dataset details and reuse information.
Wolbachia endosymbionts manipulate the self-renewal and differentiation of germline stem cells to reinforce fertility of their fruit fly host
Open the record for dataset details and reuse information.
Data from: Attractive male sticklebacks carry more oxidative DNA damage in the soma and germline
<p>Trade-offs between the expression of sexual signals and the maintenance of somatic and germline tissues are expected when these depend upon the same resources. Despite the importance of sperm DNA integrity, its trade-off with sexual signalling has rarely been explored. We experimentally tested the trade-off between carotenoid-based sexual colouration and oxidative DNA damage in skeletal muscle, testis and sperm by manipulating reproductive schedule (early <i>vs.</i> late onset of breeding) in male three-spined sticklebacks. Oxidative DNA damage was measured as the amount of 8-hydroxy-2-deoxy-Guanosine in genomic DNA. Irrespective of the experimentally manipulated reproductive schedule, individuals investing more in red colouration showed higher levels of oxidative DNA damage in muscle, testis and sperm during the peak breeding season. Our results show that the expression of red colouration traded off against the level of oxidative DNA damage possibly due to the competing functions of carotenoids as colorants and antioxidants. Thus, female sticklebacks may risk fertility and viability of offspring by choosing redder, more deteriorated partners with decreased sperm DNA integrity. The evolution of sexual signal may be constrained by oxidative DNA damage in the soma and germline. </p>
Germline proliferation trades off with lipid metabolism in Drosophila
<p>Little is known about the metabolic basis of life-history trade-offs but lipid stores seem to play a pivotal role. During reproduction, an energetically highly costly process, animals mobilize fat reserves. Conversely, reduced or curtailed reproduction promotes lipid storage in many animals. Systemic signals from the gonad seem to be involved: <em>C. elegans</em> lacking germline stem cells display endocrine changes, have increased fat stores and are long-lived. Similarly, germline-ablated <em>D. melanogaster </em>exhibit major somatic physiological changes, but whether and how germline loss affects lipid metabolism remains largely unclear. Here we show that germline-ablated flies have profoundly altered energy metabolism at the transcriptional level and store excess fat as compared to fertile flies. Germline activity thus constrains or represses fat accumulation, and this effect is conserved between flies and worms. More broadly, our findings confirm that lipids represent a major energetic currency in which costs of reproduction are paid.</p>
Integrin restriction by miR-34 protects germline progenitors from cell death during aging
<p>During aging, regenerative tissues must dynamically balance the two opposing processes of proliferation and cell death. While many microRNAs are differentially expressed during aging, their roles as dynamic regulators of tissue regeneration have yet to be described. We show that in the highly regenerative <em>Drosophila</em> testis, <em>miR-34</em> levels are significantly elevated during aging. <em>miR-34</em> modulates germ cell death and protects the progenitor germ cells from accelerated aging. However, <em>miR-34</em> is not expressed in the progenitors themselves but rather in neighboring cyst cells that kill the progenitors. Transcriptomics followed by functional analysis revealed that during aging, <em>miR-34</em> modifies integrin signaling by limiting the levels of the heterodimeric integrin receptor αPS2 and βPS subunits. In addition, we found that in cyst cells, this heterodimer is essential for inducing phagoptosis and degradation of the progenitor germ cells. Together, these data suggest that the <em>miR-34</em> – integrin signaling axis acts as a sensor of progenitor germ cell death to extend progenitor functionality during aging.</p>
IG receptor germline set for species: Mouse subgroup: 129S1/SvImJ set_name: 129S1/SvlmJ IGLV
<p>IG Germline Reference set published on the Open Germline Receptor Database (OGRDB)</p>
IG receptor germline set for species: Mouse subgroup: BALB/c/ByJ set_name: BALB/c/ByJ IGLV
<p>Germline Reference set published on the Open Germline Receptor Database (OGRDB)</p>
IG receptor germline set for species: Mouse subgroup: A/J set_name: A/J IGLV
<p>Germline Reference set published on the Open Germline Receptor Database (OGRDB)</p>
IG receptor germline set for species: Mouse subgroup: 129S1/SvImJ set_name: 129S1/SvImJ IGKV
<p>IG Germline Reference set published on the Open Germline Receptor Database (OGRDB)</p>
IG receptor germline set for species: Mouse subgroup: C3H/HeJ set_name: C3H/HeJ IGKV
<p>Germline Reference set published on the Open Germline Receptor Database (OGRDB)</p>
IG receptor germline set for species: Mouse subgroup: BALB/c set_name: BALB/c IGH
<p>Germline Reference set published on the Open Germline Receptor Database (OGRDB)</p>
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.