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Dataset results
612 results for “imprinting”
Data from: Evolution of smooth tubercle bacilli PE and PE_PGRS genes: evidence for a prominent role of recombination and imprint of positive selection
Background: PE and PE_PGRS are two mycobateria-restricted multigene families encoding membrane associated and secreted proteins that have expanded mainly in the pathogenic species, notably the Mycobacterium tuberculosis complex (MTBC). Several lines of evidence attribute to PE and PE_PGRS genes critical roles in mycobacterial pathogenicity. To get more insight into the nature of these genes, we sought to address their evolutionary trajectories in the group of smooth tubercle bacilli (STB), the putative ancestor of the clonal MTBC. Methodology/Principal Findings: By focussing on six polymorphic STB PE/PE_PGRS genes, we demonstrate significant incongruence among single gene genealogies and detect strong signals of recombination using various approaches. Coalescent-based estimation of population recombination and mutation rates (ρ and θ, respectively) indicates that the two mechanisms are of roughly equal importance in generating diversity (ρ/θ = 1.457), a finding in a marked contrast to house keeping genes (HKG) whose evolution is chiefly brought about by mutation (ρ/θ = 0.012). In comparison to HKG, we found 15 times higher mean rate of nonsynonymous substitutions, with strong evidence of positive selection acting on PE_PGRS62 (dN/dS = 1.42), a gene that has previously been shown to be essential for mycobacterial survival in macrophages and granulomas. Imprint of positive selection operating on specific amino acid residues or along branches of PE_PGRS62 phylogenetic tree was further demonstrated using maximum likelihood- and covarion-based approaches, respectively. Strikingly, PE_PGR62 proved highly conserved in present-day MTBC strains. Conclusions/Significance: Overall the data indicate that, in STB, PE/PE_PGRS genes have undergone a strong diversification process that is speeded up by recombination, with evidence of positive selection. The finding that positive selection involved an essential PE_PGRS gene whose sequence appears to be driven to fixation in present-day MTBC strains lends further support to the critical role of PE/PE_PGRS genes in the evolution of mycobacterial pathogenicity.
A Multi-Institution Study of TGFβ Imprinted, Ex Vivo Expanded Universal Donor NK Cell Infusions as Adoptive Immunotherapy in Combination With Gemcitabine and Docetaxel in Patients With Relapsed or Ref
ClinicalTrials.gov study NCT05634369. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Clinical Study Evaluating Targeted Biopsies and Cytological Imprints in Prostate Cancer
ClinicalTrials.gov study NCT01745718. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Developing Derived Induced Pluripotent Stem Cells as a Model to Understand Imprinted Disorders
ClinicalTrials.gov study NCT05214742. IPD Sharing: YES. Countries: 1. Publications: 0.
Intratumoral Injection of Standard Universal Donor Expanded Natural Killer Cells and TGF-beta Imprinted Natural Killer Cells for the Treatment of Skin Squamous Cell Carcinoma and Basal Cell Carcinoma
ClinicalTrials.gov study NCT07144384. IPD Sharing: Not stated. Countries: 1. Publications: 0.
IMPRINT VR Trainer Evaluation
ClinicalTrials.gov study NCT06861907. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Prenatal Screening for Imprinting Anomalies Implicated in Beckwith Wiedemann and Silver Russell Syndromes
ClinicalTrials.gov study NCT01842659. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Can Epimutations be Inherited? How to Manage Patients With Imprinting-related Diseases Who Wish to Become Parents
ClinicalTrials.gov study NCT02859688. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Influenza IMPRINT Cohort: Defining the Impact of Initial Influenza Exposure on Immunity in Infants
ClinicalTrials.gov study NCT05436184. IPD Sharing: NO. Countries: 1. Publications: 0.
Intestinal Microbiota in Prostate Cancer Patients as a Biomarker for Radiation-INduced Toxicity (IMPRINT)
ClinicalTrials.gov study NCT04638049. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Characterization of global loss of imprinting in overgrowth syndrome induced by assisted reproduction
GEO Series GSE63509. Bos indicus x Bos taurus. 32 samples. Type: Expression profiling by high throughput sequencing.
Bacterial skin infection imprints bone marrow eosinophils to promote allergic skin-lung crosstalk
GEO Series GSE287038. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing; Other.
Uncovering the phenotypic consequences of multi-locus imprinting disturbances using genome-wide methylation analysis in genomic imprinting disorders
GEO Series GSE237503. Homo sapiens. 19 samples. Type: Methylation profiling by array.
Epigenetic profiling at mouse imprinted gene clusters
GEO Series GSE16588. Mus musculus. 18 samples. Type: Methylation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array.
Tissue signals imprint ILC2 identity with anticipatory function [RNA-Seq]
GEO Series GSE117470. Mus musculus. 45 samples. Type: Expression profiling by high throughput sequencing.
Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells [endogenous FSCs]
GEO Series GSE79435. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (RNA-seq)
GEO Series GSE56524. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional and imprinting complexity in Arabidopsis seeds at single-nucleus resolution
GEO Series GSE157145. Arabidopsis thaliana. 1664 samples. Type: Expression profiling by high throughput sequencing.
Endogenous retroviral insertions drive non-canonical imprinting in extra-embryonic tissues [ChIP-Seq]
GEO Series GSE124212. Mus musculus. 51 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting: allele specific mRNA-seq expression profiling in Arabidopsis thaliana Col, Ler, and Cvi parental and re
GEO Series GSE52806. Arabidopsis thaliana. 30 samples. Type: Expression profiling by high throughput sequencing.
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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.