Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11870978_1.fastq.gz | Fastqsanger.gz | |||
| SRR11870979_1.fastq.gz | Fastqsanger.gz | |||
| SRR11870980_1.fastq.gz | Fastqsanger.gz | |||
| SRR11870981.fastq.gz | Fastqsanger.gz | |||
| SRR18003204_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:How humans differ from one another at the molecular level and the impact of ethnicity, age and environmental factors such as diet and geography are poorly understood. To address this gap, we analyzed 322 nominally healthy individuals from diverse ethnic backgrounds located in distinct geographical regions, using (1) deep multi-omic profiling - including genome sequencing, transcriptomics, glycomics, targeted and untargeted metabolomics, lipidomics, proteomics, 16S microbiota sequencing, metaproteomics, metallomics, and metabolic hormone and pathogen profiling, (2) clinical data collection, and (3) comprehensive lifestyle surveys. Our integrative analysis revealed several key findings: associations between molecular profiles (transcripts, proteins, metabolites, lipids, glycans, and microbiota) and age, ethnicity, and geographical residence (including diet) among healthy individuals; ethnicity-specific genetic polymorphisms in key genes governing whole-body homeostasis, particularly in lipid/carbohydrate metabolism and neuroinflammation pathways; and variation in the abundance of key proteins such as the TERF2 interacting protein (TERF2IP) which is critical for cellular aging, genome stability, and protection against chromosomal degradation. These findings hold significant translational value, particularly in understanding ethnicity as a risk factor for autoimmune diseases. Many ethnicity-associated molecules identified in our study interact with existing therapeutic drugs, highlighting the potential need for ethnicity-specific drug dosing adjustments. Furthermore, our results suggest that geographical factors influence ethnic patterns, which may, in turn, affect longevity. individuals with European ancestry exhibited a lower phenotypic age, while those of Asian ancestry showed a higher phenotypic age when living outside their ancestral regions. By providing both a comprehensive baseline dataset of multi-omic variation in healthy individuals and critical insights into the molecular basis of human diversity, our study enhances our understanding of how environmental and genetic factors influence phenotypic and molecular traits and potentially augments individualized health approaches.
2026-04-10 | PXD059114 | Pride
Project description:Glucocorticoids (GCs) are steroid hormones widely used as pharmaceutical interventions, which act mainly by regulating gene expression levels. A large fraction of patients (~30%), especially those of African descent, show a weak response to treatment. To interrogate the contribution of variable transcriptional response to inter-ethnic differences, we measured in vitro lymphocyte GC sensitivity (LGS) and transcriptome-wide response to GCs in peripheral blood mononuclear cells (PBMCs) from African-American and European-American healthy donors. We found that transcriptional response after 8hrs treatment was significantly correlated with variation in LGS within and between populations. We found that NFKB1, a gene previously found to predict LGS within populations, was more strongly downregulated in European-Americans on average. NFKB1 could not completely explain population differences, however, and we found an additional 177 genes with population differences in the average log2 fold change (FDR<0.05), most of which also showed a weaker transcriptional response in AfricanAmericans. These results suggest that inter-ethnic differences in GC sensitivity reflect variation in transcriptional response at many genes, including regulators with large effects (e.g. NFKB1) and numerous other genes with smaller effects.
2012-02-01 | GSE33649 | 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. 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:Glucocorticoids (GCs) are steroid hormones widely used as pharmaceutical interventions, which act mainly by regulating gene expression levels. A large fraction of patients (~30%), especially those of African descent, show a weak response to treatment. To interrogate the contribution of variable transcriptional response to inter-ethnic differences, we measured in vitro lymphocyte GC sensitivity (LGS) and transcriptome-wide response to GCs in peripheral blood mononuclear cells (PBMCs) from African-American and European-American healthy donors. We found that transcriptional response after 8hrs treatment was significantly correlated with variation in LGS within and between populations. We found that NFKB1, a gene previously found to predict LGS within populations, was more strongly downregulated in European-Americans on average. NFKB1 could not completely explain population differences, however, and we found an additional 177 genes with population differences in the average log2 fold change (FDR<0.05), most of which also showed a weaker transcriptional response in AfricanAmericans. These results suggest that inter-ethnic differences in GC sensitivity reflect variation in transcriptional response at many genes, including regulators with large effects (e.g. NFKB1) and numerous other genes with smaller effects. Total RNA was obtained from paired aliquots of peripheral blood mononuclear cells treated with dexamethasone or vehicle (EtOH) for 8 and 24 hours.
2012-02-01 | E-GEOD-33649 | biostudies-arrayexpress
Project description:Elucidating the genetic basis underlying the variation in hepatic gene expression is of importance to understand disease etiology and drug metabolism variances. To date, no genome-wide eQTL analysis has been conducted in the Han Chinese, the largest ethnic group in the world. We performed a genome-wide eQTL mapping in a set of Han Chinese liver tissue (n=64).
2015-01-02 | GSE53790 | GEO
Project description:The Malaysian Node of the Human Variome Project Database (MyHVPDb) is a country specific database of human variant and gene mutation that was established in 2011. This ethnic specific mutation and variation databases are being continuously updated, recording extensive information over the genetic heterogeneity of the Malaysian ethnic groups. The database comprises of SNP Database and Mutation Database. The SNP database has stored 291718 SNPs that was obtained by genotyping the SNPs of 101 healthy individuals from six Malay sub-ethnic groups which consist of Malay Kelantan, Malay Banjar, Malay Kedah, Malay Jawa, Malay Bugis and Malay Champa.
2015-02-11 | GSE65760 | GEO
Project description:VCF files with whole genome sequencing data of 49 individuals of European/Romanian descent, and 50 individuals of Roma (Romani/Rroma) ethnic background from Romania.
| EGAD00001004982 | EGA
Project description:BAM files (Illumina HiSeq 2000) with whole genome sequencing data of 49 individuals of European/Romanian descent, and 50 individuals of Roma (Romani/Rroma) ethnic background from Romania.
| EGAD00001004981 | EGA
Project description:Myanmar locates in the crossroads of South Asia, Southeast Asia, and East Asia, and is known for high culture diversity in different ethnic groups. It is considered to be important for understanding human evolutionary history and genetic diversity in East Eurasia. However, relatively few studies have examined the population structure and demographic history in Myanmar to date. In this study, we analyzed more than 220,000 genome-wide SNPs in 175 new samples of five ethnic groups from Myanmar and compared them with the published data. Our results showed that the Myanmar population is intricately substructured, with the main observed clusters corresponding roughly to western/northern highlanders (Chin, Naga, and Jingpo) and central/southern lowlanders (Bamar and Rakhine). The gene flow inferred from South Asia has a substantial influence (~11%) on the gene pool of central/southern lowlanders rather than western/northern highlanders. The genetic admixture is dated around 650 years ago. These findings suggest that the genome-wide variation in Myanmar was likely shaped by the linguistic, cultural, and historical changes.
2019-12-31 | GSE74100 | GEO