Nematode metagenome strain:from University of Washington USA
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA185210 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Normal healthy cells (monocytes, promyelocytes, polymorphonuclear cells, B cells, T cells, CD34+CD38- HSPCs) run as controls for TCGA AML marker publication. Bone marrow cells collected from healthy donors were sorted and DNA extracted at Washington University in St. Louis, microarrays were then run at USC
2013-08-07 | GSE49618 | GEO
Project description:Earthworm egg capsule microbial communities from the University of Washington, USA metagenome
| PRJNA336817 | ENA
Project description:Earthworm egg capsule microbial community from the University of Washington, USA - (E. fetida Yelm) metagenome
| PRJNA366704 | ENA
Project description:University of Washington Developmental Single Cell Atlas
| PRJNA622599 | ENA
Project description:University of Washington Developmental Single Cell Atlas
| PRJNA622600 | ENA
Project description:Washington University PDX Development and Trial Center
| PRJNA683677 | ENA
Project description:Washington University PDX Development and Trial Center
| PRJNA683678 | ENA
Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom mailto:sull@u.washington.edu). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). This track contains chromatin interaction data from the University of Washington ENCODE group generated using 5C (Chromatin Conformation Capture Carbon Copy). The 5C method is used here to define short and long-range range interactions between transcription start sites (TSS) and DNaseI hypersensitive sites (DHS) or other genomic features. The 5C method is summarized below. Transcription factors bind to promoter-associated proteins, bringing the associated DNA sequences in close proximity to each other. Cross linking the DNA and proteins immobilizes these interactions and thus maintains their close proximity. Cleavage of the sample with restriction endonuclease followed by ligation results in hybrid molecules where a fragment with a regulatory element is physically associated with a fragment containing a TSS. The interactions are then detected by oligonucleotide-dependent, ligation-mediated assays, where one set of primers is complementary to the end of fragments with a TSS and the second set of primers are complementary to fragments with a feature. Primers are designed to the forward strand of the feature and the reverse strand of the TSS so that ligation only occurs between TSS and feature, not between different features. Specific interactions are detected by massively parallel sequencing. The data in this track comprises two different experiment types focusing on targeted regions: Gene-targeted project: Analysis of DNase I hypersensitive sites reveals many genes where there are multiple sites restricted to the cell type where a protein is observed to be expressed. These sites potentially identify regulatory sites for the gene. This set of experiments attempts to observe interactions between these DHS sites and transcription starts in 25 regions selected based on genes expressed in GM06990 (B-lymphocyte), BJ (foreskin fibroblast), HepG2 (liver cancer cell line), or SK-N-SH_RA (neuroblastoma cell line, SKNSH, differentiated with retinoic acid). Myc project: Genome wide association studies have identified SNPs linked to prostate, colon, and breast cancer in the gene desert region upstream of the myc gene. 5C of HindIII fragments interacting with those containing refSeq txStarts in this region were performed in 5 cell types: GM12878 (B-lymphocyte), CaCo2 (colon cancer cell line), LNCaP (prostate cancer cell line), MCF7 (breast cancer cell line), and K562 (erythroleukemia cell line). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2012-07-19 | GSE39505 | GEO
Project description:Genome-wide DNA methylation profiling of blood of participants from a high CVD risk community-based cohort of African American individuals from Washington D.C. Chronic stress increases the risk of cardiovascular disease (CVD) and amygdalar activity (AmygA), a known marker of chronic stress which has been associated with subclinical CVD. Previous research suggests a plausible connection between AmygA, hematopoietic tissue activity, arterial inflammation, and cardiovascular events. There is a paucity of data on the relationships between AmygA, hematopoietic activity, and epigenomics modifications through deoxyribonucleic acid (DNA) methylation among racial and ethnic minorities. We investigated the association between AmygA and spleen (SpleenA) and bone marrow activity (BMA) as well as DNA methylation at genes previously associated with stress. Participants included in the study were from a high CVD risk community-based cohort of African American individuals from Washington D.C. AmygA was measured by aortic uptake of 18Fluorodeoxyglucose (FDG) on Positron Emission Tomography/Computed Tomography and calculated as standardized uptake values (SUVs). SpleenA and BMA were calculated as SUVs from regions of interest within the spleen and vertebrae, respectively. Standardized beta coefficients (β ) and p-values were calculated from linear regression models adjusted for body mass index and 10-year predicted atherosclerotic CVD risk.
2024-09-06 | GSE241763 | GEO
Project description:Center for Mendelian Genomics [CMG] - University of Washington Center for Mendelian Genomics
| PRJNA233538 | ENA