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1,666 results for “human genome”
Genomic atlas of the human proteome from brain, CSF and plasma: Improvement with TOPMed imputed genomics
<p>Abstract</p> <p>Comprehensive expression quantitative trait loci (eQTL) studies have been instrumental for understanding tissue-specific gene regulation and pinpointing functional genes for disease-associated GWAS loci in a tissue-specific manner. Compared to gene expressions, proteins more directly affect various biological processes, often dysregulated in disease, and are important drug targets. We previously performed and identified tissue-specific protein QTL (pQTL) in neurologically relevant tissues. We now enhance this work by analyzing more proteins (1,300 versus 1,079) and an almost twofold increase in high-quality imputed genetic variants (8.4 million versus 4.4 million) by using TOPMed reference panel. We identified 38 genomic regions associated with 43 proteins in brain, 150 regions associated with 247 proteins in CSF, and 95 regions associated with 145 proteins in plasma. Compared to our previous study, this study newly identified 12 pQTL in brain, 30 pQTL in CSF, and 22 pQTL in plasma. Our improved genomic atlas uncovers the genetic control of protein regulation across multiple tissues. These pQTL findings are assessable through the Online Neurodegenerative Trait Integrative Multi-Omics Explorer (ONTIME) for use by the scientific community.</p>
Genomic atlas of the human proteome from brain, CSF and plasma: Improvement with TOPMed imputed genomics
<p>Abstract</p> <p>Comprehensive expression quantitative trait loci (eQTL) studies have been instrumental for understanding tissue-specific gene regulation and pinpointing functional genes for disease-associated GWAS loci in a tissue-specific manner. Compared to gene expressions, proteins more directly affect various biological processes, often dysregulated in disease, and are important drug targets. We previously performed and identified tissue-specific protein QTL (pQTL) in neurologically relevant tissues. We now enhance this work by analyzing more proteins (1,300 versus 1,079) and an almost twofold increase in high-quality imputed genetic variants (8.4 million versus 4.4 million) by using TOPMed reference panel. We identified 38 genomic regions associated with 43 proteins in brain, 150 regions associated with 247 proteins in CSF, and 95 regions associated with 145 proteins in plasma. Compared to our previous study, this study newly identified 12 pQTL in brain, 30 pQTL in CSF, and 22 pQTL in plasma. Our improved genomic atlas uncovers the genetic control of protein regulation across multiple tissues. These pQTL findings are assessable through the Online Neurodegenerative Trait Integrative Multi-Omics Explorer (ONTIME) for use by the scientific community.</p>
Genomic atlas of the human proteome from brain, CSF and plasma: Improvement with TOPMed imputed genomics
<p>Abstract</p> <p>Comprehensive expression quantitative trait loci (eQTL) studies have been instrumental for understanding tissue-specific gene regulation and pinpointing functional genes for disease-associated GWAS loci in a tissue-specific manner. Compared to gene expressions, proteins more directly affect various biological processes, often dysregulated in disease, and are important drug targets. We previously performed and identified tissue-specific protein QTL (pQTL) in neurologically relevant tissues. We now enhance this work by analyzing more proteins (1,300 versus 1,079) and an almost twofold increase in high-quality imputed genetic variants (8.4 million versus 4.4 million) by using TOPMed reference panel. We identified 38 genomic regions associated with 43 proteins in brain, 150 regions associated with 247 proteins in CSF, and 95 regions associated with 145 proteins in plasma. Compared to our previous study, this study newly identified 12 pQTL in brain, 30 pQTL in CSF, and 22 pQTL in plasma. Our improved genomic atlas uncovers the genetic control of protein regulation across multiple tissues. These pQTL findings are assessable through the Online Neurodegenerative Trait Integrative Multi-Omics Explorer (ONTIME) for use by the scientific community.</p>
Genomic atlas of the human proteome from brain, CSF and plasma: Improvement with TOPMed imputed genomics
<p>Abstract</p> <p>Comprehensive expression quantitative trait loci (eQTL) studies have been instrumental for understanding tissue-specific gene regulation and pinpointing functional genes for disease-associated GWAS loci in a tissue-specific manner. Compared to gene expressions, proteins more directly affect various biological processes, often dysregulated in disease, and are important drug targets. We previously performed and identified tissue-specific protein QTL (pQTL) in neurologically relevant tissues. We now enhance this work by analyzing more proteins (1,300 versus 1,079) and an almost twofold increase in high-quality imputed genetic variants (8.4 million versus 4.4 million) by using TOPMed reference panel. We identified 38 genomic regions associated with 43 proteins in brain, 150 regions associated with 247 proteins in CSF, and 95 regions associated with 145 proteins in plasma. Compared to our previous study, this study newly identified 12 pQTL in brain, 30 pQTL in CSF, and 22 pQTL in plasma. Our improved genomic atlas uncovers the genetic control of protein regulation across multiple tissues. These pQTL findings are assessable through the Online Neurodegenerative Trait Integrative Multi-Omics Explorer (ONTIME) for use by the scientific community.</p>
Human genome assemblies enhanced by LOCLA
<p>This is a data repository for the genome assemblies of three human samples enhanced by LOCLA (DOI: 10.5281/zenodo.8280853 ). LOCLA is a novel genome assembly optimization tool, LOCLA, that iteratively improves the quality of an assembly by locating sequencing reads on partially assembled scaffolds and thus enable gap filling and further scaffolding. </p> <p>The three human genome assemblies and the assembly statistics are compressed into one single zip file. File names are explained as follows:</p> <ol> <li>LLD0021C_locla.fasta : Whole genome assembly of a Taiwanese male individual generated by LOCLA</li> <li>LLD0021C_locla_quality.txt : Assembly statistics of LLD0021C_locla.fasta</li> <li>chm13_locla.fasta : Whole genome assembly of the CHM13 cell line generated by LOCLA</li> <li>chm13_locla_quality.txt : Assembly statistics of chm13_locla.fasta</li> <li>hg002_gma_locla.fasta : Whole genome assembly of the HG002 sample generated by LOCLA </li> <li>hg002_gma_locla_quality.txt : Assembly statistics of hg002_gma_locla.fasta</li> </ol> <p> </p>
CTCF BINDING PATTERNS DEFINE TADS AND BOUNDARY ELEMENTS IN HUMAN AND MOUSE GENOMES
<p><em><strong>Msci thesis from Industrial Placement at Politecnico di Milano</strong></em></p> <p> </p> <p><strong>Abstract</strong></p> <p>In eukaryotes, the genome is highly packaged inside the nucleus. This hierarchical structure requires complex compartmentation and organization. Topologically associating domains (TADs) serve as architectural units in the 3D genome, functioning to regulate and constrain gene interaction. TAD boundaries are enriched in the CCCTC-binding factor (CTCF). Due to the asymmetric nature of the CTCF motif, it exhibits differing orientations based on the strand it is localized. Motif orientation is crucial for loop formation, which is facilitated in a convergent orientation. While the relationship between TADs and CTCF motif patterns has been described in humans, the model remained to be corroborated in other mammals. </p> <p>We conducted a comparative analysis by applying the research conducted in humans to the mouse genome. By integrating ChIP-seq data, we examined the CTCF sites based on ChIP-seq peak consolidation, signal value, and motif p-value. This analysis aimed to comprehend the binding profile of CTCF and elucidate its complexity in terms of binding strength and cross-tissue conservation. Mouse genome CTCF motifs were categorized into cluster patterns based on their relative orientation. Following this classification, the distribution of each pattern was studied using ChIP-seq-related descriptors. We then built a TAD boundary collection based on the insulation score. Boundary consolidation and length, insulation score, and CTCF number were used to reconcile CTCF to TAD boundary function. The cluster patterns were then mapped to TAD and TAD boundaries to elucidate their structure based on the spatial arrangement of CTCF.</p> <p>The distribution of ChIP-seq-validated CTCF sites within TAD boundaries revealed a well-defined structure, characterized by an abundance of the divergent pattern. Boundaries with the highest insulation scores exhibited both a high consolidation and CTCF enrichment. This set of boundaries was used to study TAD structure. An increment of the convergent pattern was observed inside TADs. The individual CTCF sites on the interior of the TAD were further organized into left and right sections, corresponding to an opposing directional arrangement to TAD boundaries. Significantly, the ChIP-seq data contained many unannotated peaks and non-signal motifs. These were associated with a high motif p-value, low ChIP-seq signal, low consolidation, and a less structured arrangement of CTCF clustering. Moreover, non-signal motifs were underrepresented within TAD boundaries and displayed a disorderly distribution.</p> <p>The human model of CTCF-dependent TAD structure was confirmed in mice. The model suggested the inherent alternation between convergent and divergent patterns, with these CTCF sites conferring characteristic properties upon TADs and their boundaries. These traits encompass the change of preferential genomic interaction and boundary insulation capability. Thus, the orientation-based clustering of CTCF sites was further validated as a good method to define TADs in a precise organized manner.</p>
Computationally defined and in vitro validated putative genomic safe harbour loci for transgene expression in human cells
<p>Selection of the target site is an inherent question for any project aiming for directed transgene integration. Genomic safe harbour (GSH) loci have been proposed as safe sites in the human genome for transgene integration. Although several sites have been characterised for transgene integration in the literature, most of these do not meet criteria set out for a GSH, and the limited set that do have not been characterised extensively. Here, we conducted a computational analysis using publicly available data to identify 25 unique putative GSH loci that reside in active chromosomal compartments. We validated stable transgene expression and minimal disruption of the native transcriptome in three GSH sites <em>in vitro</em> using human embryonic stem cells (hESCs) and their differentiated progeny. Furthermore, for easily targeted transgene expression, we have engineered constitutive landing pad expression constructs into the three validated GSH in hESCs.</p>
GROVER tokenized Human Genome hg19
<p>Data of the Human Genome Hg19, tokenised with byte-pair tokenisation of 600 cycles. Required for the DNA language model GROVER. More information can be found at https://www.biorxiv.org/content/10.1101/2023.07.19.549677v1.</p>
Dataset for "Comprehensive Identification of NUMTs in the Human Reference Genome through Pan-Mitogenome"
<p><strong>存放"Comprehensive Identification of NUMTs in the Human Reference Genome through Pan-Mitogenome"文章中的相关数据。</strong></p> <p>包括blastn出来的原始output文件;mtDNA-like short segments fastq文件;ATAC-seq的fastq文件;</p> <p>以及文章中提及的supplementary 表格和bed文件</p>
Ancient genomes from Bronze Age remains reveal deep diversity and recent adaptive episodes for human oral pathobionts
<p>Supporting data for "Ancient genomes from Bronze Age remains reveal deep diversity and recent adaptive episodes for human oral pathobionts"</p>
Genomic Responses of Human Immune and Non-Immune Cells to Glucocorticoids
ClinicalTrials.gov study NCT02798523. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Canine genome-wide association study identifies DENND1B as an obesity gene in dogs and humans
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Assessing changes in genomic divergence following a century of human mediated secondary contact among wild and captive-bred ducks
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Genomes and associated scripts for paper: Potential millennial-scale avian declines by humans in southern China
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A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances
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Footprint of the host restriction factors APOBEC3 on the genome of human viruses
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Computationally defined and in vitro validated putative genomic safe harbour loci for transgene expression in human cells
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Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya
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Data from: Transcriptional regulation of human <em>NMNAT2</em>: Insights from 3D genome sequencing and bioinformatics
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Data from: Genomic signatures of adaptation in native lizards exposed to human-introduced fire ants
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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.