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2,168 results for “deletion”

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zenodo48/100

PopDel identifies medium-size deletions jointly in tens of thousands of genomes - Variant call sets

This data set contains the variant calls sets generated by different tools for the benchmarks in the paper <a href="https://www.nature.com/articles/s41467-020-20850-5">PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes</a>. It includes the VCFs/BCFs for the following test cases: <ul> <li>Random deletion simulation on up to 1000 chromosome 21 samples</li> <li>1000 Genomes Project deletions inserted into simulated chromosomes 17 to 22 of up to 500 samples</li> <li>HG001 (NA12878)</li> <li>Trio of <a href="https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/">HG002</a> + <a href="https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG003_NA24149_father/NIST_HiSeq_HG003_Homogeneity-12389378/">HG003</a> + <a href="https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG004_NA24143_mother/NIST_HiSeq_HG004_Homogeneity-14572558/">HG004</a></li> <li><a href="https://github.com/Illumina/Polaris/wiki/HiSeqX-Diversity-Cohort">Polaris Diversity cohort</a></li> <li><a href="https://github.com/Illumina/Polaris/wiki/HiSeqX-Kids-Cohort">Polaris Kids cohort</a></li> </ul> Further, the long and short read reference call sets for HG001 are provided. For HG002 the reference call set and the high confidence regions by the Genome in a Bottle consortium are provided. For details on how the files have been created, please refer to the paper and the script repository on <a href="https://github.com/kehrlab/PopDel-scripts">GitHub</a>.

opencc-by-4.0Aug 2020View details →

zenodo44/100

Deletion of porcine BOLL causes defective acrosomes and subfertility in Yorkshire boars

This datset contains plink binaries (final_recode_ID.bed, final_recode_ID.bim, final_recode_ID.fam) that contain array-derived genotypes for 35 Yorkshire boars. 12 boars produced sperm with defective acrosomes. The case/control status (1-unaffected; 2-affected) of the 35 boars is indicated in the accompanying phenotype file (final_recode_ID.pheno). The corresponding pre-print is at the bioRxiv: https://biorxiv.org/cgi/content/short/2020.05.05.074724v1

opencc-by-4.0May 2020View details →

zenodo44/100

Gene tagging and gene deletion resources for Leishmania mexicana MNYC/BZ/62/M379 Cas9/T7 strain

primers_barcodes.csv: List of primer sequences necessary for N and C terminus gene tagging, as well as gene deletion in the Leishmania mexicana MNYC/BZ/62/M379 Cas9/T7 strain. Each row contains the gene name and the DF (downstream forward), DR (downstream reverse), DSG (downstream guide sRNA), UF (upstream forward), UFB (upstream forward including a gene-unique 17nt barcode sequence), UR (upstream reverse), USG (upstream guide sRNA), VF (verification forward) and VR (verification reverse) primer sequences. Empty cells indicate that it was not possible to design this primer for this gene. Guide sRNA perfect match and off-target counts are included as well. The primer sequences were designed using LeishGEdit (http://www.leishgedit.net). Barcode sequences and assigned IDs for the unique identification of knock-out or tagged strains are included as separate columns. For recommended methods for endogenous tagging or gene deletion see Beneke et al., R. Soc. Open Sci.4170095 (2017), for generating barcoded deletion mutants see Beneke and Gluenz, Mol. Biochem. Parasitol. 239 (2020). genome.gff: Annotated genome of the L. mexicana MNYC/BZ/62/M379 strain, genetically modified to express T7 RNA polymerase and Cas9. The annotation is provided in a combined GFF3 / FASTA format that also includes the sequences of the chromosomes and small contigs. The annotation also specifies polyadenylation sites (PAS features) and splice leader acceptor sites (SLAS features) which were used to refine the boundaries of protein-coding sequences as well as 3' and 5' untranslated regions over the reference genome of L. mexicana MNYC/BZ/62/M379. c9t7_sequences.fasta: Raw chromosome and contig sequences in FASTA format. c9t7_transcripts.fasta: mRNA transcript sequences in FASTA format (includes 5' and 3' UTRs). c9t7_transcript_CDSs.fasta: Coding sequences in FASTA format. c9t7_predicted_protein_sequences.fasta: Predicted protein amino acid sequences in FASTA format. Note: This version provides an update for c9t7_transcript_CDSs.fasta, c9t7_predicted_protein_sequences.fasta and genome.gff, correcting an off-by-one sequence coordinate in 48 of the the protein-coding genes.

opencc-by-4.0Jul 2022View details →

dryad40/100

Data for: Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells

Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets. To identify signaling differences that may contribute to these developmental defects, an unbiased phospho-(p)-proteome screen was performed. Surprisingly, despite the genetic heterogeneity, hundreds of shared p-peptides were identified between autism subtypes including the mTOR pathway. mTOR signaling alterations were confirmed in all NPCs across both ASD subtypes and mTOR modulation rescued ASD phenotypes and reproduced autism NPC-associated phenotypes in control NPCs. Thus, our studies demonstrate that genetically distinct ASD subtypes have common defects in neurite outgrowth and migration which are driven by the shared pathogenic mechanism of mTOR signaling dysregulation.

opencc-zeroMar 2024View details →

dryad40/100

β-cell-specific deletion of Zfp148 improves nutrient-stimulated β-cell Ca2+ responses

Insulin secretion from pancreatic β-cells is essential for glucose homeostasis. An insufficient response to the demand for insulin results in diabetes. We previously showed that β-cell-specific deletion of Zfp148 (β-Zfp148KO) improves glucose tolerance and insulin secretion in mice. Here, we performed Ca2+ imaging of islets from β‑Zfp148KO and control mice on both a chow and a Western-style diet. β-Zfp148KO islets demonstrate improved sensitivity and sustained Ca2+ oscillations in response to elevated glucose. β-Zfp148KO islets also exhibit elevated sensitivity to amino acid-induced Ca2+ influx under low glucose conditions, suggesting enhanced mitochondrial phosphoenolpyruvate (PEP)-dependent KATP channel closure, independent of glycolysis. RNA sequencing and proteomics of β-Zfp148KO islets revealed altered levels of enzymes involved in amino acid metabolism (SLC3A2, SLC7A8, GLS, GLS2, PSPH, PHGDH, PSAT1) and intermediary metabolism (GOT1, PCK2), consistent with altered PEP cycling. In agreement with this, β-Zfp148KO islets displayed enhanced insulin secretion in response to L-glutamine and activation of glutamate dehydrogenase. Understanding pathways controlled by ZFP148 may provide promising strategies for improving β-cell function that are robust to the metabolic challenge imposed by a Western diet.

opencc-zeroMay 2022View details →

zenodo40/100

Dataset of the deleted DOIs extracted from the difference set between Crossref DOIs as of March 2017 and January 2021

Abstract Digital Object Identifiers (DOIs) are regarded as persistent; however, they are sometimes deleted. Deleted DOIs are an important issue not only for persistent access to scholarly content but also for bibliometrics, because they may cause problems in correctly identifying scholarly articles. However, little is known about how much of deleted DOIs and what causes them. We identified deleted DOIs by comparing the datasets of all Crossref DOIs on two different dates, investigated the number of deleted DOIs in the scholarly content along with the corresponding document types, and analyzed the factors that cause deleted DOIs. Using the proposed method, 708,282 deleted DOIs were identified. The majority corresponded to individual scholarly articles such as journal articles, proceedings articles, and book chapters. There were cases of many DOIs assigned to the same content, e.g., retracted journal articles and abstracts of international conferences. We show the publishers and academic societies which are the most common in deleted DOIs. In addition, the top cases of single scholarly content with a large number of deleted DOIs were revealed. The findings of this study are useful for citation analysis and altmetrics, as well as for avoiding deleted DOIs.   Data Records The data format of the dataset is JSON lines, where each line is a single record. In this dataset, we identified the deleted DOIs by from the difference set between Crossref DOIs as of March 2017 and January 2021. We note that the file "00_Non-Crossref_DOIs.jsonl.gz" is not deleted DOIs but other files are deleted DOIs. Please refer the conference paper shown in the references for details. Sample of the record is the following. <ul> <li>doi -- DOI name (String), e.g., "10.xxxx/xxxx"</li> <li>whichRA -- Registration agency name or error message for the DOI name according to the “<a href="https://www.doi.org/factsheets/DOIProxy.html#whichra">whichRA?</a>.” (String). "Airiti," "Crossref," "DOI does not exist," "DataCite," "KISTI," "Public," or "mEDRA."</li> <li>redirects -- Redirected URIs for the DOI name obtained by curl command (Array of String), e.g., ["https://doi.org/10.1001/archinte.166.4.387","http://archinte.jamanetwork.com/article.aspx?doi=10.1001/archinte.166.4.387"]</li> <li>redirect_to_other_doi -- The other DOI when the DOI link redirects to. (Array of String), e.g., "[10.1001/archinte.166.4.387]"</li> <li>timestamp -- Date the data was retrieved  (Datetime), "2022-01-30T02:10:45Z"</li> <li>label -- The group where the DOI belongs to. Alias DOIs," "DOIs with Deleted Description in Metadata," "DOIs without Redirects," "Defunct DOIs," "Non-Crossref DOIs," "Non-existing DOIs," or  "Other DOIs."</li> </ul> As for the file "04_DOIs_with_Deleted_Description_on_Metadata.jsonl.gz," additional records are available as follows. <ul> <li>alias_doi  -- Alias DOI name, the same as the value of "doi." (String), e.g., "10.1007/bf00400428."</li> <li>primary_doi -- Primary DOI name for the alias DOI name, the same as the first value of "redirect_to_other_doi". (String), e.g., "10.1007/bf00400429"</li> <li>container_title_of_alias_doi -- the container title for the alias DOI according to the Crossref REST API. e.g., "CrossRef Listing of Deleted DOIs."</li> <li>title_of_alias_doi --  the title for the alias DOI according to the Crossref REST API. e.g., "CrossRef Listing of Deleted DOIs."</li> <li>container_title_of_primary_doi -- the container title for the primary DOI according to the Crossref REST API. e.g., "CrossRef Listing of Deleted DOIs."</li> <li>title_of_alias_doi --  the title for the primary DOI according to the Crossref REST API. e.g., "CrossRef Listing of Deleted DOIs."</li> </ul> References <ul> <li>Kikkawa, J., Takaku, M. & Yoshikane, F. "Analysis of the deletions of DOIs: What factors undermine their persistence and to what extent?", Proceedings of the 26th International Conference on Theory and Practice of Digital Libraries (<a href="http://tpdl2022.dei.unipd.it/">TPDL 2022</a>), (to appear), 2022.</li> </ul> FUNDING <ul> <li>JSPS KAKENHI Grant Number <a href="https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-21K21303">JP21K21303</a>, <a href="https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-22K18147">JP22K18147</a>, <a href="https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-20K12543">JP20K12543</a>, and <a href="https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-21K12592">JP21K12592</a></li> </ul>

opencc-by-4.0Jul 2022View details →

zenodo40/100

BCL6 deletion in CD4 T cells reveals Th2 eff mediated immunity in the skin

RNA-Seq datasets related to the study of Mouse Tfh cells. Recent studies propose that Group 2 T follicular helper (Tfh) cells have a higher degree of functional plasticity in addition to their well-defined roles in mediating IL-4-dependent switching of germinal centre B cells to the production of IgG1 and IgE antibodies. In particular Tfh cells have been proposed to be an essential stage in Th2 effector cell development that are able to contribute to innate Type 2 responses. We used CD4-cre targeted deletion of BCL6 to identify the contribution Tfh cells make to tissue Th2 effector responses in models of skin atopic disease   and lung immunity to parasites. Ablation of Tfh cells did not impair the development or recruitment of Th2 effector subsets to the skin and did not alter the transcriptional expression profile or functional activities of the resulting tissue resident Th2 effector cells. However, the accumulation of Th2 effector cells in lung Th2 responses was partially affected by BCL6 deficiency. These data indicate that the development of Th2 effector cells does not require a BCL6 dependent step implying Tfh and Th2 effector populations follow separate developmental trajectories and Tfh cells do not contribute to Type 2 responses in the skin . This study reveals important findings that add to the growing literature around the plasticity and functional interconversion of T helper subsets.

opencc-by-4.0Sep 2022View details →

dryad40/100

Data from: Deletion of an sRNA primes development in a multicellular bacterium

Small non-coding RNAs (sRNAs) are essential in regulating gene expression during many biological processes. The myxobacteria gene pxr encodes an sRNA known to block fruiting-body development, an aggregative multicellular process triggered by starvation. Deletion of pxr allows Myxococcus xanthus cells to develop in the presence of nutrients. However, potential Pxr binding targets and most genes regulated by Pxr remain unknown. Here, we found that the absence of pxr expression dramatically alters the temporal dynamics of development, thus suggesting an important new role of this sRNA in myxobacterial ecology. We transcriptionally profiled vegetative cells of M. xanthus strains possessing vs lacking pxr and found that over half of the genes impacted by pxr deletion during growth are linked to development, including known and potentially novel critical regulators. Many other genes are associated with general metabolic processes, which Pxr regulates positively. Our study discovers new phenotypic effects of Pxr regulation of likely ecological importance, identifies the suite of genes this sRNA controls during vegetative growth, reveals a previously unknown developmental regulator and provides new insights into the early molecular regulation of myxobacterial development.

opencc-zeroMay 2024View details →

dryad40/100

Cross-species analysis identifies mitochondrial dysregulation as a functional consequence of the schizophrenia-associated 3q29 deletion

The 1.6Mb deletion at chromosome 3q29 (3q29Del) is the strongest identified genetic risk factor for schizophrenia, but the effects of this variant on neurodevelopment are not well understood. We interrogated the developing neural transcriptome in two experimental model systems with complementary advantages: isogenic human cortical organoids and isocortex from the 3q29Del mouse model. We profiled transcriptomes from isogenic cortical organoids that were aged for 2 months and 12 months, as well as perinatal mouse isocortex, all at single-cell resolution. Systematic pathway analysis implicated dysregulation of mitochondrial function and energy metabolism. These molecular signatures were supported by analysis of oxidative phosphorylation protein complex expression in mouse brains and assays of mitochondrial function in engineered cell lines. Together these data indicate that metabolic disruption is associated with 3q29Del and is conserved across species.

opencc-zeroJun 2024View details →

dryad40/100

Uncovering structural plasticity of Enterovirus A through deep insertional and deletional scanning

Insertions and deletions (InDels) are essential sources of novelty in protein evolution. In RNA viruses, InDels cause dramatic phenotypic changes that contribute to the emergence of viruses with altered immune profiles and host engagement. This work aims to comprehensively quantify the mutational tolerance of an RNA virus to insertion, deletion, and substitution. Using Enterovirus A71 (EV-A71) as a prototype for the Enterovirus A species (EV-A) of picornaviruses, we engineered approximately 45,000 insertions, 6,000 deletions, and 41,000 amino acid changes across the 2,193 coding positions of the EV-A71 proteome, quantifying their effects on viral fitness and comprehensively mapping evolutionary constraint across the viral proteome. In contrast with amino acid changes, the vast majority of InDels are lethal to virus growth. Most that are tolerated reside at a few hotspot regions. These tolerant sites highlight structurally flexible and mutationally plastic regions of EV-A71 proteins that avoid core structural and functional elements, but often overlap with key sites of host- and immune recognition, suggesting a complex evolutionary role for InDels and substitutions at these sites. Phylogenetic analysis examining EV-A species isolated from diverse mammalian hosts reveals that many of the experimentally identified hotspots also correspond to sites of natural InDel diversity across the more diverse EV-A species, suggesting these hotspots of mutational tolerance in EV-A genomes may have contributed to past phenotypic diversification of EV-A. Insights from this and future mutational scanning studies mapping viral evolutionary potential will inform better epidemiological monitoring and Enterovirus vaccine development.

opencc-zeroJun 2024View details →

zenodo40/100

ASIC2 Deletion in Medial Prefrontal Cortex Enhances Social Dominance in Mice

Social dominance is essential for maintaining a stable social society and has well-established positive and negative impacts on sociable animals, including humans. However, the regulatory mechanisms governing social dominance, as well as the crucial regulators and biomarkers involved, remain poorly understood. We discover that mice lacking acid-sensing ion channel 2 (ASIC2) exhibit a persistent higher social dominance ranking compared to their wild-type cagemates. Conversely, the overexpression of ASIC2 in the medial prefrontal cortex (mPFC) reverses the dominance hierarchy observed in ASIC2 knockout mice. ASIC2 deletion prolongs the inactivation time of ASICs, resulting in enhanced ASIC-dependent synaptic transmission and plasticity in the mPFC through the protein kinase A signaling pathway. Furthermore, ASIC2 exhibits distinct functional roles in excitatory and inhibitory neurons, thereby modulating the balance of neuronal activities underlying social dominance behaviors—a phenomenon suggestive of a cell-subtype-specific mechanism. Finally, this research establishes a foundational understanding of the mechanisms governing social dominance formation, offering potential insights for the management or prevention of social disorders, such as depression and anxiety.

opencc-by-4.0Nov 2023View details →

zenodo40/100

BRAIN Journal-High Performance Data mining by Genetic Neural Network-Figure 5. Insertion and Deletion Hidden Layer in NN

Change in NN structure is other method that we used to optimization of solution[18]. Insertion a hidden layer caused to mutation operator is much natural. As connection with father and mother nodes is easily[20],[21]. Weights of node and errors automatically calculated. For each stage of the implementation of the mutation operator in genetic algorithms, neural networks, only one of the nodes in the hidden layer is selected and inserted. These layers are inserted on condition that the definition does not harm the network structure and the action is meaningful. As an added layer can adjust the weights and the connection to the parent node of a network layer to be removed.

opencc-by-4.0Oct 2013View details →

dryad40/100

Age-specific effects of deletions: Implications for ageing theories

Evolution of ageing requires mutations with late-life deleterious effects. Classic theories assume these mutations either have neutral (Mutation Accumulation) or beneficial (Antagonistic Pleiotropy) effects early in life, but it is also possible that they start out as mildly harmful and gradually become more deleterious with age. Despite a wealth of studies on the genetics of ageing, we still have a poor understanding of how common mutations with age-specific effects are and what ageing theory they support. To advance our knowledge on this topic we measure a set of genomic deletions for their heterozygous effects on juvenile performance, fecundity at three ages, and adult survival. Most deletions have age-specific effects, and these are commonly harmful late in life. Many of the deletions assayed here would thus contribute to ageing if present in a population. Taking only age-specific fecundity into account, some deletions support Antagonistic Pleiotropy, but the majority of them better fit a scenario where their negative effects on fecundity become progressively worse with age. Most deletions have a negative effect on juvenile performance, a fact which strengthens the conclusion that deletions primarily contribute to ageing through negative effects that amplify with age.

opencc-zeroNov 2022View details →

zenodo40/100

Global effects of deletion of the sdh genes, encoding succinate dehydrogenase, and of cobalt on protein abundance in stationary phase Salmonella enterica serovar Typhimurium.

A common strategy that bacteria utilize to increase their survival under stressful conditions in their natural environments, including antibiotic treatment, is the entry into quiescence, a state of reversible cell growth arrest that offers protection against many environmental insults. Understanding quiescence is an important fundamental question, with relevance in the medical and environmental fields. Little is known about the molecular and physiological determinants that orchestrate survival during this temporary arrest of proliferation, or those that allow a rapid transition back to the proliferating state when conditions again become favorable. In the wide host-range pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) and other Gram-negative bacteria, this temporary arrest of proliferation induces the expression of the alternative sigma subunit of RNA polymerase, σS/RpoS, which remodels global gene expression to reshape the cell physiology and ensure survival under starvation and various stress conditions (i.e., the general stress response). One important aspect of persistence is the phenotypic differentiation of quiescent populations into sub-population(s) of "persisters" that survive in the presence of lethal concentrations of antibiotics. This phenomenon is worsening the worldwide antibiotic crisis, by causing therapy failure and chronic infections and potentially favoring the development of antibiotic resistance. Understanding mechanisms governing bacterial persisters is thus an important topic and a key issue for drug developments. However, despites many studies, the physiological and molecular mechanisms controlling the formation of persisters are poorly understood and controversial. We have recently discovered an unexpected functional interaction between σS and succinate dehydrogenase (Sdh) in the formation of persisters. Succinate dehydrogenase (Sdh), a membrane bound complex that connects the TCA cycle and respiratory chain, is one major target down regulated by σS (Levi-Meyrueis et al. 2014, 2015, Lago et al. 2017). Stationary-phase Salmonella grown in LB rich medium form persisters with a higher frequency than actively growing bacteria, after transfer to fresh LB medium in the presence of lethal concentrations of ampicillin and ciprofloxacin, but not significant effect of the ΔrpoS mutation on this phenomenon was observed. Surprisingly however, the ΔrpoS mutation suppressed the defect in persister formation of a Δsdh mutant. It is very likely that the ΔrpoS mutation compensates for a metabolic perturbation provoked by the Δsdh mutation, and key for persister formation. To get further insights into the synthetic rescue process involved in persisters formation, we used a mass spectrometry-based proteomics approach to compare the proteome of the wild-type, ΔrpoS, Δsdh and ΔsdhΔrpoS strains grown to late stationary phase in nutrient-rich LB medium. Cells were also grown in LB supplemented with cobalt to pinpoint major changes induced by cobalt on the Salmonella proteome. Indeed, the synthetic rescue process involved in persisters formation in the presence of ampicillin was abolished when the inoculum has been grown in the presence of a non-lethal dose of cobalt (100 μM). Accession number.The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD043726. See also: NOREL, F., & MONTEIL, V. (2023). Unraveling a synthetic rescue process involved in persisters formation [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10277562 Phégnon, L., Uttenweiler-Joseph, S., & Létisse, F. (2024). Key physiological and metabolic characteristics for the differentiation of quiescent Salmonella's cells into persisters [Data set]. Zenodo. <a href="https://doi.org/10.5281/zenodo.10885905" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10885905</a> This work was supported by the French National Research Agency (ANR-19-CE44-0005-01, PERIOMET project). References Levi-Meyrueis C, Monteil V, Sismeiro O, Dillies MA, Monot M, Jagla B, et al. Expanding the RpoS/sigmaS-network by RNA sequencing and identification of sigmaS-controlled small RNAs in Salmonella. PloS one. 2014;9(5):e96918. Levi-Meyrueis C, Monteil V, Sismeiro O, Dillies M-A, Kolb A, Monot M et al. Repressor activity of the RpoS/sigmaS-dependent RNA polymerase requires DNA binding. Nucleic Acids Res 2015 43, 1456–1468. Lago M, Monteil V, Douche T, Guglielmini J, Criscuolo A, Maufrais C, et al. Proteome remodelling by the stress sigma factor RpoS/sigma(S) in Salmonella: identification of small proteins and evidence for post-transcriptional regulation. Scientific reports. 2017;7(1):2127.

opencc-by-4.0Aug 2023View details →

dryad40/100