13413 results for ""60+mice"+"6+weeks"+diet+study+2014+2017+DOI"

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• Common Fund (CF) Genotype-Tissue Expression Project (GTEx)

  Lay Description The aim of the Genotype-Tissue Expression (GTEx) Project is to increase our understanding of how changes in our genes affect human health and disease with the ultimate goal of improving health care for future generations. GTEx will create a database that researchers can use to study how inherited changes in genes lead to common diseases. GTEx researchers are studying genes in different tissues obtained from many different people. The GTEx project also includes a study of the GTEx donor consent process - this study will help ensure that the consent process and other aspects of the project effectively address the concerns and expectations of participants in the study. GTEx is a pioneering project that uses state-of-the-art protocols for obtaining and storing a large range of organs and tissues, and for testing them in the lab. Until now, no project has analyzed genetic variation and expression in as many tissues from the same person in such a large population as planned for GTEx. Scientific Description Understanding the role of variation in the human genome is crucial to elucidating genetic contributions to human health and disease. Despite the results of genome-wide association studies (GWAS) documenting strong statistical associations between genetic variation and human traits, the functional role for most of these variants is largely unexplained. Nearly 90% of these GWAS-implicated sites lie outside of protein-coding sequences, suggesting that these variants might regulate gene expression. The goal of the Genotype-Tissue Expression (GTEx) project is to establish a resource database and tissue biobank in which to study the relationship between genetic variation and gene expression and other molecular phenotypes in reference/non-diseased tissues. The ultimate resource will include approximately 960 post-mortem donors with several dozen tissues from each, a resource large enough to study both cis- and trans- gene expression quantitative trait loci (eQTLs). Some tissue will also be banked for additional molecular analyses. To request biosamples, please see the Biobank page for more information. GTEx was initially funded as a 2-year pilot project by the NIH Common Fund (CF) in 2010, and has been scaled up after demonstration of feasibility. The project will collect and analyze RNA levels in many different human tissues and each donor will be characterized for germline genetic variation through dense genotyping arrays and sequencing of either whole exomes or whole genomes. By treating RNA expression levels as quantitative traits, eQTLs will be identified as sites containing genetic variation that correlate with changes in RNA expression. Such eQTLs have been associated with 4%-12% of expressed human genes, and with common complex human diseases, including obesity, atherosclerosis, type 2 diabetes, Crohn's disease, and asthma. Additionally, few studies have examined the tissue specificity of eQTLs. A subset of banked tissue samples will also be analyzed for other molecular phenotypes, such as DNA methylation, DNaseI hypersensitivity sites, and proteomics. The GTEx project will thus serve as a resource database and tissue bank for many future studies, especially for understanding the functional basis of inherited susceptibility to disease. All GTEx releases since Version 5 follow the NIH Genomic Data Sharing (GDS) Policy whereby there are no restrictions on use or publication after release. Additional information about the GTEx Data Release and Publication policy can be found on the GTEx Data Portal at www.gtexportal.org.

  Study phs000424

• GSA pilot raw data

  Unfiltered genotype data for a pilot study (Batch 1) of 1,140 DDD Study participants (and 12 "Empty" samples). Samples include 380 mothers, 382 fathers and 378 probands, and form 376 trios. Most of the probands have been previously genoyped on the llumina HumanCoreExome BeadChip (EGAD00010001598) or the Illumina InfiniumCoreExome Beadchip (EGAD00010001600). All samples were genotyped on the Illumina Global Screening Array.

  Dataset EGAD00010002567

• Family-Based Study on Ulcerative Colitis with Whole Exome Sequencing

  Genetic risk factors for ulcerative colitis are not well understood. We performed a family-based whole exome sequencing analysis to identify potential causal mutations. In the proband, we found a heterozygous de novo mutation in the gene HSPA1L. Our results indicate that the de novo mutation in HSPA1L is associated with ulcerative colitis.

  Study phs001251

• Sex Differences in MAGEL2 Gene Promoter Methylation in High Functioning Autism - Trends from a Pilot Study Using Nanopore Cas9 Targeted Long Read Sequencing

  Using DNA extracted from peripheral blood, Cas9-targeted nanopore DNA sequencing was used to analyze MAGEL2 gene, including its entire regulatory construct (chr15:23639316-23651466), for sequence variation and 5-methyl-cytosine (5mC) modification in a cohort of adults with HFA compared to sex- and age-matched NC.

  Study EGAS50000000508

• Pilot study towards the development of a Companion/Complimentary Diagnosis platform using liquid biopsy with cfDNA for immune checkpoint inhibitor therapy in advanced urothelial cancer

  Preliminary analysis was conducted to develop a cfDNA-based platform capable of predicting gene mutation profiles, TMB, gene expression profiles (molecular subtype diagnosis), and immunohistochemical findings (PD-L1 expression) using the primary lesion tissue of bladder cancer and upper urinary tract epithelial cancer, verifying the feasibility of such development.

  Study JGAS000714

• RNA-seq from B-ALL patients treated on the ALLG ALL09 study

  Dataset contains RNA-sequencing data (fastq files) from 46 patients treated on the Australasian Leukaemia and Lymphoma Group (ALLG) ALL09 study (ACTRN12618001734257). All patients were diagnosed with CD19 positive B-cell acute lymphoblastic leukaemia and were negative for Philadelphia chromosome positive disease. Patient samples (bone marrow or peripheral blood) were taken at diagnosis. mRNA was extracted from lymphoblasts and underwent paired-end sequencing using either the illumina NextSeq (75 bp PE) or MGI DNABSEQ-G400 (100bp PE) platforms. Transcriptomic data was used for identification of genomic drivers of acute lymphoblastic leukaemia (ALL).

  Dataset EGAD50000001603

• single nuclei multiomics (ATAC-RNA) of KOLF2.1J human induced pluripotent stem cells-derived differentiated dopaminergic neurons

  We processed nuclei from hIPSCs differentiated optimized protocols for generating dopaminergic neurons. Cells differentiated with a first iteration were RNA and ATAC-sequenced, to understand our protocol caveats to address for optimization. Cells differentiated with a second protocol and in vivo were RNA-sequenced to validate the identities of our cells.

  Study EGAS50000001418

• R compatible Seurat's objetc .rds files with count data and metadata from single cell RNA seq analysis to characterize the prostate cancer tumoral microenviroment of 31 fusion biopses.

  Pre-processed Seurat objects with cellular and functional annotation information from the scRNAseq study on PC fusion biopsy samples. The data consists of rds files composed of normalised counts matrices, normalised and scaled counts, functional enrichment counts at the cellular level and metadata with patient grouping and cellular annotation variables. There are 3 .rds files, one with the total cells (SCP_data_analysis), with the selection of cells annotated as cancerous (selected_cancer_analysis) and cancer-associated fibroblasts (selected_caf_analysis).

  Dataset EGAD50000001298

• Spinocerebellar ataxia type 3 RNA-sequencing study

  RNA-Sequencing from human post-mortem Spinocerebellar ataxia type 3 patients. This sequencing experiment was carried out to validate that the transcriptional changes of an Ataxin-3 knock-in mouse model (expressing an expansion of 304 CAG/CAAs either heterozygous or homozygous in the murine Ataxin-3 locus) represent that transcriptional changes seen in the human disease.

  Study EGAS00001004241

• ADAPTeR Study: scRNA and scTCR data from TILs from two ccRCC patients treated with anti-PD1

  TILs were extracted from two ccRCC patients treated with (Nivolumab) anti-PD1, one was responsive to treatment, the other non-responsive. IgG4 staining was used to separate cells into anti-PD1 bound and unbound, the samples then underwent paired scRNA and scTCR sequencing on the 10x Genomics platform.

  Study EGAS00001005640