259 results for ""independent+of+the+choice+of+kernel"+regularization+parameter+volumetric+rendering+paper"

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• CRISPR iPSC methods paper

  This submission is of the sequencing data used in the CRISPR iPSC methods paper. Specifically it is 3 fastq files that each represent a replicate of an experiment to transduce the Toronto KnockOut CRISPR Library - Version 3 (TKOv3) into inferred pluripotent stem cell (iPSC) derived macrophages. The sequencing is of the guide RNAs from the TKOv3 having been extracted from the transduced iPSC derived macrophages.

  Dataset EGAD00001007020

• RNA-Seq data for AEL paper

  Dataset EGAD00001003412

• Whole exome data for AEL paper

  Dataset EGAD00001003413

• National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS)

  NIAGADS is an NIH controlled-access data repository that collaborates with researchers around the world to facilitate data access and sharing for genomic and associated omics data related to Alzheimer's Disease (AD), Alzheimer's Disease Related Dementias (ADRD), as well as healthy aging. Serving as the data coordinating center for the Alzheimer's Disease Sequencing Project (ADSP), NIAGADS hosts all ADSP-generated whole-exome, whole-genome and associated phenotypes. Other data types hosted by NIAGADS include genotype SNP arrays, functional omics, fluid biomarkers, aggregated imaging data (such as volumetric data for brain regions of interest), and summary statistics. In adherence with NIH security best practices and genome data sharing policies, NIAGADS supports data access requests through review by an NIH-appointed and registered Data Access Committee. Data stored within NIAGADS cannot be requested via dbGaP. Data requests must go through the NIAGADS Data Sharing Service (DSS) via the following NIAGADS url: https://dss.niagads.org/. Questions related to the request of data should be directed to the NIAGADS admin team at: niagads@pennmedicine.upenn.edu. DSS is a FISMA certified platform built by a team of data scientists at the University of Pennsylvania to support the request and access of AD/ADRD data by qualified researchers internationally. Questions related to the use of data hosted in the DSS should be directed to the Portal admin team at: help@niagads.org.

  Study phs004180

• Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity

  We studied a patient with recurrent respiratory infections and hypogammaglobulinemia and identified a germline homozygous missense mutation in IKZF2 encoding Helios (p.Ile325Val). We show that HeliosI325V retains DNA-binding and dimerization properties, but loses interaction with several partners, including epigenetic remodelers HDAC1, HDAC3 and the ATAC complex. Single-cell RNA-sequencing of peripheral blood mononuclear cells revealed gene expression signatures indicative of a shift towards pro-inflammatory, effector-like status in the patient’s T cells. We observed an upregulation of the anti-inflammatory gene, TSC22D3, encoding the glucocorticoid-induced leucine zipper (GILZ), whose expression was reported to increase upon IL-2 deprivation. We validated this finding in primary T cells, where we observed a pronounced reduction in IL-2 production upon their stimulation, together with a defect in their ability to proliferate, rendering them more anergic. Collectively, we identify a novel germline-encoded inborn error of immunity and define a role for Helios in conventional T cells, whereby interactions with specific binding partners is necessary to mediate the transcriptional programs that enable T-cell homeostasis in health and disease.

  Study EGAS00001005675

• Gtag&T single-cell genome and transcriptome data

  This submission contains single-cell genome and transcriptome data that is used for the following manuscript: https://doi.org/10.1101/2023.01.13.521174. All Illumina data deposited here is retrieved from HCC38(BL) cell lines and a melanoma PDX model as described in the paper.

  Study EGAS00001007043

• Data for paper Mold, Weissman et al. 'Clonally heritable gene expression imparts a layer of diversity within cell types'

  Dac EGAC50000000102

• Genomic Data Archive From the Network for Pancreatic Organ Donors With Diabetes

  The Network for Pancreatic Organ Donors with Diabetes (nPOD) is the largest biorepository of human pancreata from organ donors with type 1 diabetes (T1D), maturity-onset diabetes of the young (MODY), cystic fibrosis-related diabetes (CFRD), type 2 diabetes (T2D), gestational diabetes, and islet autoantibody positive (AAb+)/pre-T1D. The mission of the nPOD is to distribute biospecimens and associated de-identified data/metadata to an international researcher network, and to promote the development of new treatments for these diabetes conditions. Here, we describe the release of high-parameter genotyping data for the nPOD cohort. Specifically, 372 subjects were genotyped using a customized precision medicine single nucleotide polymorphism (SNP) microarray (UFDIchip). These data were technically validated using published algorithms to evaluate donor relatedness, ancestry, imputed HLA, and T1D genetic risk score. Additionally, 207 subjects were queried for rare known and novel coding region variants via whole exome sequencing (WES). These data are now publicly available, enabling genotype-selected sample requests and the study of novel genotype : phenotype associations, ultimately to explain diabetes heterogeneity and inform precision medicine strategies to interrupt diabetes pathogenesis.

  Study phs002861

• NGS WGS Data - Unic TDP

  WGS data from the Unicorn-PASS cohort for the Tandem Duplicator Phenotype paper

  Dataset EGAD50000001567

• Highlighted samples from the BCH CRDC

  These exomes are from some of the patients and family members detailed in our forthcoming publication, Children’s Rare Disease Cohorts: an integrative research and clinical genomics initiative. While this paper details an institutional collection of exomes, the samples here were specifically highlighted as having significant findings.

  Study EGAS00001004436