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.
2,168
datasets available to search
ShareScore release 0.9.0
Dataset results
2,168 results for “deletion”
Early onset of adult deafness in the Rhodesian Ridgeback is associated with in-frame deletion in the EPS8L2 gene
Open the record for dataset details and reuse information.
Alu-Mediated MEN1 Gene Deletion and Loss of Heterozygosity in a Patient with Multiple Endocrine Neoplasia Type 1
<p>Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder caused by mutations of the tumor suppressor gene <i>MEN1</i>. Most of the germline <i>MEN1</i> gene mutations have been small mutations, and the whole gene deletion is rarely observed. In the present study, we revealed <i>Alu </i>retrotransposon-mediated <i>de novo</i> germline deletion of the whole <i>MEN1</i> gene and somatic copy-neutral loss of heterozygosity (LOH) in a patient with MEN1. The patient is a 39-year-old woman who was referred to our department for the management of prolactinoma. She was also diagnosed with primary hyperparathyroidism and suspected of MEN1. Although nucleotide sequencing did not detect any <i>MEN1</i> gene mutations, multiplex ligation-dependent probe amplification (MLPA) revealed a large germline deletion of the <i>MEN1</i> gene. Subsequent quantitative polymerase chain reaction (qPCR)-based copy number mapping showed a monoallelic loss of approximately 18.5-kilobase region containing the whole <i>MEN1</i> gene. Intriguingly, the two breakpoints were flanked by <i>Alu</i> repetitive elements, suggesting the contribution of <i>Alu</i>/<i>Alu</i>-mediated rearrangements to the whole <i>MEN1 </i>gene deletion. Furthermore, copy number mapping using MLPA and qPCR in combination with single nucleotide polymorphism analysis revealed copy-neutral LOH as a somatic event for parathyroid tumorigenesis. In conclusion, copy number mapping revealed a novel combination of <i>Alu</i>/<i>Alu</i>-mediated <i>de novo</i> germline deletion of the <i>MEN1</i> gene and somatic copy-neutral LOH as a cytogenetic basis for the MEN1 pathogenesis. Moreover, subsequent <i>in silico</i> analysis highlighted the possible predisposition of the <i>MEN1 </i>gene to <i>Alu </i>retrotransposon-mediated genomic deletion.</p>
Raw diffraction images of hollow-forming cypovirus polyhedra mutant crystals (H3L2 deletion)
<p>Crystal structure of cypovirus polyhedra mutant (H3L2 deletion) to form hollow inside (PDB code: <a href="https://www.rcsb.org/structure/6LEE">6LEE</a>).</p> <p>Small-wedge (5° or 10°/each) datasets were collected from loop-harvested microcrystals using <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md">EIGER</a> X 9M detector at a wavelength of 1 Å using a microbeam on BL32XU, SPring-8. </p> <p>All diffraction images were processed using XDS through <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/kamo-en.md">KAMO</a> pipeline, and merged using XSCALE with kamo.multi_merge. The crystals belong to space group I23 with a=103.8 Å. Finally 45 datasets were merged at 1.95 Å resolution in the published result. </p>
Data from: Mining for single nucleotide polymorphisms and insertions / deletions in expressed sequence tag libraries of oil palm
The oil palm is a tropical oil bearing tree. Recently EST-derived SNPs and SSRs are a free by-product of the currently expanding EST (Expressed Sequence Tag) data bases. The development of high-throughput methods for the detection of SNPs (Single Nucleotide Polymorphism) and small indels (insertion / deletion) has led to a revolution in their use as molecular markers. Available (5452) Oil palm EST sequences were mined from dbEST of NCBI. CAP3 program was used to assemble EST sequences into contigs. Candidate SNPs and Indel polymorphisms were detected using the perl script auto_snip version 1.0 which has used 576 ESTs for detecting SNPs and Indel sites. We found 1180 SNP sites and 137 indel polymorphisms with frequency 1.36 SNPs / 100 bp. Among the six tissues from which the EST libraries had been generated, mesocarp had high frequency of 2.91 SNPs and indels per 100 bp whereas the zygotic embryos had lowest frequency of 0.15 per 100 bp. We also used the Shannon index to analyze the proportion of ten possible types of SNP/indels. ESTs from tissues of normal apex showed highest values of Shannon index (0.60) whereas abnormal apex had least value (0.02). The present report deals the use of Shannon index for comparing SNP/ indel frequencies mined from ESTlibraries and also confirm that the frequency of SNP occurrence in oil palm to use them as markers for genetic studies.
Data from: Recurrent gene deletions and the evolution of adaptive cyanogenesis polymorphisms in white clover (Trifolium repens L.)
Understanding the molecular evolution of genes that underlie intraspecific polymorphisms can provide insights into the process of adaptive evolution. For adaptive polymorphisms characterized by gene presence/absence (P/A) variation, underlying loci commonly show signatures of long-term balancing selection, with gene-presence and gene-absence alleles maintained as two divergent lineages. We examined the molecular evolution of two unlinked P/A polymorphisms that underlie a well-documented adaptive polymorphism for cyanogenesis (hydrogen cyanide release with tissue damage) in white clover. Both cyanogenic and acyanogenic plants occur in this species, and the ecological forces that maintain this chemical defense polymorphism have been studied for several decades. Using a sample of 65 plants, we investigated the molecular evolution of sequences flanking the two underlying cyanogenesis genes: Ac/ac (controlling the presence/absence of cyanogenic glucosides), and Li/li (controlling the presence/absence of their hydrolyzing enzyme, linamarase). A combination of genome-walking, PCR assays, DNA sequence analysis, and Southern blotting was used to test whether these adaptive P/A polymorphisms show evidence of long-term balancing selection, or whether gene-absence alleles have evolved repeatedly through independent deletion events. For both loci, we detect no signatures of balancing selection in closest flanking genomic sequences. Instead, we find evidence for variation in the size of the deletions characterizing gene-absence alleles. These observations strongly suggest that both of these polymorphisms have been evolving through recurrent gene deletions over time. We discuss the genetic mechanisms that could account for this surprising pattern and the implications of these findings for mechanisms of rapid adaptive evolution in white clover.
live cell super-resolution data_dual_color_cell_line_CTCF_E-2_deletion
Open the record for dataset details and reuse information.
Correction of multiexon deletion mutation in human dystrophin by Cas12i editing
<p>Because the file exceeds 200 MB, these supplementary files are uploaded to <a href="https://zenodo.org/"><strong>Zenodo</strong></a>. </p>
Raw data to: "Vaccine-elicited CD4 T cells prevent the deletion of antiviral B cells in chronic infection"
<p>Raw data underlying the publication by Narr et al. entitled "Vaccine-elicited CD4 T cells prevent the deletion of antiviral B cells in chronic infection".</p>
Adult-Onset Deletion of ATP13A2 in Mice Induces Progressive Nigrostriatal Pathway Dopaminergic Degeneration and Lysosomal Abnormalities
Open the record for dataset details and reuse information.
Deleted Dataset
Open the record for dataset details and reuse information.
THE DONALD TRUMP CASE AND THEBIG TECH: THE PERMANENT DELETION OF ACCOUNTS ON SOCIAL NETWORKS ANALYZED FROM THE BRAZILIAN CONSTITUTIONAL PERSPECTIVE
Open the record for dataset details and reuse information.
Fig. 6 Bayesian Inference relationships obtained for all the trnD1–4 in An exceptional case of mitochondrial tRNA duplication-deletion events in blood-feeding leeches
Fig. 6 Bayesian Inference relationships obtained for all the trnD1–4 sequences known to date
Fig. 5 Maximum Likelihood inferred relationships for all the trnD1–4 in An exceptional case of mitochondrial tRNA duplication-deletion events in blood-feeding leeches
Fig. 5 Maximum Likelihood inferred relationships for all the trnD1–4 sequences known to date
Circuit mechanism underlying fragmented sleep and memory deficits in 16p11.2 deletion mouse model of autism
Open the record for dataset details and reuse information.
Genome deletions and rewiring of the transcriptome underlie high antimonite resistance in Achromobacter sp. SMAs-55
Open the record for dataset details and reuse information.
Utilizing insights of DNA repair machinery to discover MMEJ deletions and novel mechanisms
<p><span>We developed Del-read, an algorithm targeting medium-sized deletions (6-100 bp) in short-reads, which are challenging for current variant callers relying on alignment. Our focus was on Micro-Homolog mediated End Joining deletions (MMEJ-dels), prevalent in myeloid malignancies. MMEJ-dels follow a distinct pattern, occurring between two homologies, allowing us to generate a comprehensive list of MMEJ-dels in the exome. Using Del-read, we identified numerous novel germline and somatic MMEJ-dels in BEAT- AML and TCGA-breast datasets. Validation in 672 healthy individuals confirmed their presence. These novel MMEJ-dels were linked to genomic features associated with replication stress, like G-quadruplexes and minisatellite. <a name="_Hlk170686758"></a>Additionally, we observed a new category of MMEJ-dels with an imperfect match at the flanking sequences of the homologies, suggesting a mechanism involving mispairing in homology alignment. We demonstrated robustness of the repair system despite CRISPR-Cas9-induced mismatches in the homologies. Further analysis of the canonical ASXL1 deletion revealed a diverse array of these imperfect matches. This suggests a potentially more flexible and error-prone MMEJ repair system than previously understood. Our findings highlight Del-read's potential in uncovering previously undetected deletions and deepen our understanding of repair mechanisms.</span></p>
Data from: Impaired hippocampal place cell dynamics in a mouse model of the 22q11.2 deletion
Hippocampal place cells represent the cellular substrate of episodic memory. Place cell ensembles reorganize to support learning but must also maintain stable representations to facilitate memory recall. Despite extensive research, the learning-related role of place cell dynamics in health and disease remains elusive. Using chronic two-photon Ca2+ imaging in hippocampal area CA1 of wild-type and Df(16)A+/− mice, an animal model of 22q11.2 deletion syndrome, one of the most common genetic risk factors for cognitive dysfunction and schizophrenia, we found that goal-oriented learning in wild-type mice was supported by stable spatial maps and robust remapping of place fields toward the goal location. Df(16)A+/− mice showed a significant learning deficit accompanied by reduced spatial map stability and the absence of goal-directed place cell reorganization. These results expand our understanding of the hippocampal ensemble dynamics supporting cognitive flexibility and demonstrate their importance in a model of 22q11.2-associated cognitive dysfunction.
An ensemble deep learning framework to refine large deletions in linked-reads
<p>An ensemble deep learning framework to refine large deletions in linked-reads</p>
Figure 2 from: Alvarado AT, Muñoz AM, Bartra MS, Valderrama-Wong M, González D, Quiñones LA, Varela N, Bendezú MR, García JA, Loja-Herrera B (2021) Frequency of CYP1A1*2A polymorphisms and deletion of the GSMT1 gene in a Peruvian mestizo population. Pharmacia 68(4): 747-754. https://doi.org/10.3897/pharmacia.68.e71621
Figure 2 Genotypic analysis of CYP1A1*2A and GSTM1 (-) (2% agarose gel). Std represents the 100 bp molecular weight marker. The 340 bp amplicon represents the undigested CYP1A1 gene fragment. The 200 bp and 140 bp fragments correspond to the fragments cut with the enzyme Mspl. The 273 bp amplicon corresponds to the presence of GSTM1.
Phosphoproteomics profiling of mice with genetic deletions in Ku70
<p>Phosphoproteomics data for WT, Ku70 +/- and Ku70 -/- mice.</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.