GNPS_Humulus_lupulus_cone_development
Ontology highlight
ABSTRACT:
INSTRUMENT(S): micrOTOF-Q II
ORGANISM(S): Humulus Lupulus (ncbitaxon:3486)
SUBMITTER: 
Birger L. Moller
PROVIDER: MSV000095961 | GNPS |
REPOSITORIES: GNPS
Similar Datasets
Project description:This study was to collect expression level polymorphism (ELP) data for the barley genotypes Steptoe and Morex, parents of a widely used North American mapping population. Primarily, the data collected will show the amount of variation between these genotypes in seedling leaves grown in a greenhouse at the same time, with replications on three separate dates. ----------------------------------------------------------------------------------------------------------------------- Roger P. Wise(Head of Lab) and Stacy Barkeloo are the original contributors of this experimental data. PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of them . The equivalent experiment is 'BB16' at PLEXdb. Keywords: genotype
2008-05-27 | GSE11182 | GEO
Project description:There is extensive variation in DNA methylation between individuals and ethnic groups. These differences can arise from a combination of genetic and non-genetic influences and potential modifiers include nutritional cues, early life experience, and social and physical environments. Here we have assayed genome-wide DNA methylation in neonatal cord blood from African American, European American, and other ancestral groups. This is part of the CANDLE Study (Conditions Affecting Neurocognitive Development and Learning in Early Childhood). Our overarching goal is to determine the different environmental and maternal factors that can modify DNA methylation in newborns.
2015-01-14 | GSE64940 | GEO
Project description:This study was to collect expression level polymorphism (ELP) data for the barley genotypes Steptoe and Morex, parents of a widely used North American mapping population. Primarily, the data collected will show the amount of variation between these genotypes in seedling leaves grown in a greenhouse at the same time, with replications on three separate dates. -----------------------------------------------------------------------------------------------------------------------; Roger P. Wise(Head of Lab) and Stacy Barkeloo are the original contributors of this experimental data. PLEXdb(www.plexdb.org) has submitted this series at GEO on behalf of them . The equivalent experiment is 'BB16' at PLEXdb. Experiment Overall Design: genotype: Steptoe(3-replications); genotype: Morex(3-replications)
2008-06-18 | E-GEOD-11182 | biostudies-arrayexpress
Project description:There is extensive variation in DNA methylation between individuals and ethnic groups. These differences can arise from a combination of genetic and non-genetic influences and potential modifiers include nutritional cues, early life experience, and social and physical environments. Here we have assayed genome-wide DNA methylation in neonatal cord blood from African American, European American, and other ancestral groups. This is part of the CANDLE Study (Conditions Affecting Neurocognitive Development and Learning in Early Childhood). Our overarching goal is to determine the different environmental and maternal factors that can modify DNA methylation in newborns. This is a cross-sectional study of a total of 216 racially diverse participants of CANDLE. Cordblood was collected at birth. DNA methylation was measured using the Illumina HumanMethylation27 BeadChip. Based on maternal self-report, the samples are 112 African Americans, 91 European Americans and 13 other racial or mixed race group.
2015-01-14 | E-GEOD-64940 | biostudies-arrayexpress
Project description:The incidence and mortality rates of prostate cancer are significantly higher in African-American men when compared to European-American men. We tested the hypothesis that differences in tumor biology contribute to this survival health disparity. Using microarray technology, we obtained gene expression profiles of primary prostate tumors resected from 33 African-American and 36 European-American patients. These tumors were matched on clinical parameters. We also evaluated 18 non-tumor prostate tissues from 7 African-American and 11 European-American patients. The resulting datasets were analyzed for expression differences on the gene and pathway level comparing African-American with European-American patients. Our analysis revealed a significant number of genes, e.g., 162 transcripts at a false-discovery rate less than 5%, to be differently expressed between African-American and European-American patients. Using a disease association analysis, we identified a common relationship of these transcripts with autoimmunity and inflammation. These findings were corroborated on the pathway level with numerous differently expressed genes clustering in immune response, stress response, cytokine signaling, and chemotaxis pathways. Furthermore, a two-gene tumor signature was identified that accurately differentiated between African-American and European-American patients. This finding was confirmed in a blinded analysis of a second sample set. In conclusion, the gene expression profiles of prostate tumors indicate prominent differences in tumor immunobiology between African-American and European-American men. The profiles portray the existence of a distinct tumor microenvironment in these two patient groups. Keywords: Microdissected tissue analysis
2008-01-01 | GSE6956 | GEO
Project description:To investigate genetic and molecular differences that may exist between prostate cancers of African American and European American origin. Gene expression profile analysis was performed comparing RNA seq data of African American prostate cancer cell lines (inhouse) and European American prostate cancer cell lines (public repository)
2022-08-05 | GSE203338 | GEO
Project description:Purpose: The goal of the current study was to find the candidate genes responsible for the habita specific clock variation in N. discreta. Methods: We performed RNA-seq experiment using four strains ; African parent (FGSC8831), North American parent (FGSC 8578) and two representative progeny representing African clock phenotype (N309-89) and North American clock phenotype (N309-50). Results: We identified one candidate gene that meets our criteria; confirmed it's expression by qPCR and it's expression pattern is associated with parent genotype. Conclusions: Our approach using the expression profiles and SNP data of two parents and two representative progeny led us to identify a candidate gene for a complex clock adaptation phenotype.
2018-09-18 | GSE120053 | GEO
Project description:The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture.
2012-04-18 | GSE37342 | GEO
Project description:The incidence and mortality rates of prostate cancer are significantly higher in African-American men when compared to European-American men. We tested the hypothesis that differences in tumor biology contribute to this survival health disparity. Using microarray technology, we obtained gene expression profiles of primary prostate tumors resected from 33 African-American and 36 European-American patients. These tumors were matched on clinical parameters. We also evaluated 18 non-tumor prostate tissues from 7 African-American and 11 European-American patients. The resulting datasets were analyzed for expression differences on the gene and pathway level comparing African-American with European-American patients. Our analysis revealed a significant number of genes, e.g., 162 transcripts at a false-discovery rate less than 5%, to be differently expressed between African-American and European-American patients. Using a disease association analysis, we identified a common relationship of these transcripts with autoimmunity and inflammation. These findings were corroborated on the pathway level with numerous differently expressed genes clustering in immune response, stress response, cytokine signaling, and chemotaxis pathways. Furthermore, a two-gene tumor signature was identified that accurately differentiated between African-American and European-American patients. This finding was confirmed in a blinded analysis of a second sample set. In conclusion, the gene expression profiles of prostate tumors indicate prominent differences in tumor immunobiology between African-American and European-American men. The profiles portray the existence of a distinct tumor microenvironment in these two patient groups. Experiment Overall Design: A total of 69 fresh-frozen prostate tumors were obtained from the NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) and the Department of Pathology at the University of Maryland (UMD). All tumors were resected adenocarcinomas that had not received any therapy prior to prostatectomy. The macro-dissected CPCTR tumor specimens (n = 59) were reviewed by a CPCTR-associated pathologist, who confirmed the presence of tumor in the specimens. These tissues were collected between 2002 and 2004 at four different sites, with each site providing tissues from both African-American and European-American patients. Information on race/ethnicity (33 African-Americans and 36 European-Americans) was either extracted from medical records (CPCTR) or obtained through an epidemiological questionnaire in which race/ethnicity was self-reported (UMD). Only one patient, a European-American, was also Hispanic. Surrounding non-tumor prostate tissue was collected from 18 of the recruited patients in this study. Of those, 7 were African-American men and 11 were European-American men. We also isolated total RNA from 10 needle biopsy specimens collected from patients at the National Naval Medical Center (one African-American and 9 European-Americans) that did not have prostate cancer. From those, we prepared two RNA pools, each representing 5 patients. Clinicopathological characteristics of the patients, including age at prostatectomy, histology, Gleason score, pathological stage, PSA at diagnosis, tumor size, extraprostatic extension, margin involvement, and seminal vesicle invasion were obtained from CPCTR. For UMD cases, this information was extracted from the medical and pathology records, if available. Written informed consent was obtained from all donors. Tissue collection and study design were approved by the institutional review boards of the participating institutions.
2008-06-15 | E-GEOD-6956 | biostudies-arrayexpress
Project description:The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture. 204 samples were analysed with the Illumina platform Human610-Quad v 1.0 and are described herein.
2012-04-17 | E-GEOD-37342 | biostudies-arrayexpress