PAGE: Global Reference Panel
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ABSTRACT:
PROVIDER: PRJNA302341 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:<p>Stanford contributed samples to the PAGE study that can act as a population reference dataset across the globe. Therefore this dataset includes reference individuals, without phenotypes, chosen to help infer ancestry that will help us understand the diverse samples available in PAGE. The complete dataset comprises individuals of European, African, Asian, Oceanian, and Native American descent, from a total of over 50 populations. A subset of these individuals from Puno, Peru and Easter Island (Rapa Nui), Chile, are included in the PAGE samples that were whole genome sequenced in 2015. Additional details are available in the Study Acknowledgments.</p> <p>The Global Reference Panel comprises 6 sample sets: <ul><li>A population sample of Andean individuals primarily of Quechuan/Aymaran ancestry from Puno, Peru</li> <li>A population sample of Easter Island (Rapa Nui), Chile</li> <li>Individuals of indigenous origin from Oaxaca, Mexico</li> <li>Individuals of indigenous origin from Honduras</li> <li>Individuals of indigenous origin from Colombia</li> <li>Individuals of indigenous origin from the Nama and Khomani KhoeSan populations of the Northern Cape, South Africa</li></ul> </p> <p>In addition, we genotyped publicly available samples that will be hosted on the Bustamante lab website (<a href="https://bustamantelab.stanford.edu/">https://bustamantelab.stanford.edu/</a>). These comprise large public datasets to provide an open reference dataset for the world:</p> <p> <ul><li>The additional related individuals from the Americas in the Human Genome Diversity Panel (H952) plus all additional samples from the Americas</li> <li>A subset of the unrelated individuals from the Maasai in Kinyawa, Kenya (MKK) dataset from the International Hapmap Project hosted at Coriell</li></ul> </p> <p>Additional samples will be available for restricted use with a data access agreement with the Bustamante Lab.</p> <p>This study is part of the Population Architecture using Genomics and Epidemiology (PAGE) study (<a href="./study.cgi?study_id=phs000356">phs000356</a>). </p>
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Project description:Characterization of the reference epigenome in humans in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues **************** For data usage terms and conditions, please refer to: http://www.nida.nih.gov/about/roadmap/epigenomics/data_access_policies.html **************** BI Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project. EDACC Genboree Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSTUDY%2FEDACC.4057
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Project description:Genome scale characterization of chromatin modification, RNA expression, and cytosine methylation in a diverse panel of primary human cells and tissues, stem cells, and iPS cells derived from deidentified human subjects **************** For data usage terms and conditions, please refer to: http://www.nida.nih.gov/about/roadmap/epigenomics/data_access_policies.html **************** BI Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project. EDACC Genboree Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSTUDY%2FEDACC.3212
2010-11-12 | E-GEOD-25249 | biostudies-arrayexpress
Project description:Gene Expression Networks in the Drosophila Genetic Reference Panel
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Project description:We report a large-scale transcriptomic analysis of several tissues of a reference Drosophila melanogaster strain as well as 141 Drosophila Genetic Reference Panel (DGRP) lines at high temporal resolution. Comprehensive data analysis has identified thousands of genes under clock- and tissue-specific control. By using a molecular time table approach, we uncovered that >20% of probed DGRP lines exhibit aberrant circadian expression, and the genetic dissection of one line (DGRP-796) revelled disrupted circadian gene expression in all analysed tissues, revealing a novel deletion in the cry gene. Together, this study revealed extensive variation in tissue-specific circadian expression, which acts upon tissue-specific regulatory networks to generate local oscillations in gene expression. Moreover, the many other lines identified here can be now used to better understand the mechanisms underlying the molecular clock, from tissue-specific to more central mechanisms.
2020-12-10 | GSE126018 | GEO
Project description:Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of the human proteome, as well as exhibit a stable protein composition in different batches of sample regeneration. Previously, The Clinical Proteomic Tumor Analysis Consortium (CPTAC) utilized PDX-derived comparative reference (CompRef) materials for the longitudinal assessment of proteomic performance, however, inherent drawbacks of PDX-derived material has resulted in efforts to identify a new source of CompRef material. In this study, we examined the utility of using a panel of seven cancer cell lines, NCI-7 Cell Line Panel, as a reference material for mass spectrometric analysis of the human proteome. Our results showed that not only is the NCI-7 material suitable for benchmarking laboratory sample preparation methods, but NCI-7 sample generation is highly reproducible at both the global and phosphoprotein levels. In addition, the predicted genomic and experimental coverage of the NCI-7 proteome suggests the NCI-7 material may also have applications as a universal standard proteomic reference.
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Project description:Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of the human proteome, as well as exhibit a stable protein composition in different batches of sample regeneration. Previously, The Clinical Proteomic Tumor Analysis Consortium (CPTAC) utilized a PDX-derived comparative reference (CompRef) materials for the longitudinal assessment of proteomic performance; however, inherent drawbacks of PDX-derived material, including extended time needed to grow tumors and high level of expertise needed, have resulted in efforts to identify a new source of CompRef material. In this study, we examined the utility of using a panel of seven cancer cell lines, NCI-7 Cell Line Panel, as a reference material for mass spectrometric analysis of human proteome. Our results showed that not only is the NCI-7 material suitable for benchmarking laboratory sample preparation methods, but also NCI-7 sample generation is highly reproducible at both the global and phosphoprotein levels. In addition, the predicted genomic and experimental coverage of the NCI-7 proteome suggests the NCI-7 material may also have applications as a universal standard proteomic reference.
<ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/study-summary/S041">https://cptac-data-portal.georgetown.edu/study-summary/S041</a> on 12/08/21</li></ul>
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