CeD_UnitedKingdom
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010001767 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Asthma is caused by a combination of poorly understood genetic and environmental factors. We found multiple markers on chromosome 17q21 to be strongly and reproducibly associated with childhood onset asthma in family and case-referent panels with a combined P < 10-12. In independent replication studies the 17q21 locus showed strong association with diagnosis of childhood asthma in 2,320 subjects from a cohort of German children (P = 0.0003) and in 3,301 subjects from the British 1958 Birth Cohort (P = 0.0005). We systematically evaluated the relationships between markers of the 17q21 locus and transcript levels of genes in EBV-transformed lymphoblastoid cell lines from children in the asthma family panel used in our association study. The SNPs associated with childhood asthma were consistently and strongly associated (P <10-22) in cis with transcript levels of ORMDL3, a member of a gene family that encode transmembrane proteins anchored in the endoplasmic reticulum. The results indicate that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma. Keywords: association study, global gene expression, asthma, ORMDL3
2007-07-01 | GSE8052 | GEO
Project description:Asthma is caused by a combination of poorly understood genetic and environmental factors. We found multiple markers on chromosome 17q21 to be strongly and reproducibly associated with childhood onset asthma in family and case-referent panels with a combined P < 10-12. In independent replication studies the 17q21 locus showed strong association with diagnosis of childhood asthma in 2,320 subjects from a cohort of German children (P = 0.0003) and in 3,301 subjects from the British 1958 Birth Cohort (P = 0.0005). We systematically evaluated the relationships between markers of the 17q21 locus and transcript levels of genes in EBV-transformed lymphoblastoid cell lines from children in the asthma family panel used in our association study. The SNPs associated with childhood asthma were consistently and strongly associated (P <10-22) in cis with transcript levels of ORMDL3, a member of a gene family that encode transmembrane proteins anchored in the endoplasmic reticulum. The results indicate that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma. Experiment Overall Design: Gene expression levels were evaluated in 404 children. We then evaluated the relationship between SNPs in the 17q21 region (which show association to asthma in the same children) with gene expression levels. See http://www.sph.umich.edu/csg/liang/asthma/
2007-11-09 | E-GEOD-8052 | biostudies-arrayexpress
Project description:CTCF ChIP-seq of 39 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011059 (dataset).
2023-08-31 | E-MTAB-13117 | biostudies-arrayexpress
Project description:H3K27ac ChIP-seq of 79 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, 4 samples derived from CD34+ cord blood cells of healthy donors were included. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011060 (dataset).
2023-08-31 | E-MTAB-13119 | biostudies-arrayexpress
Project description:Embryonic genome activation (EGA) marks the onset of embryonic program and enables the transition toward the first lineage specification. However, the molecular features of EGA and the transcription factors (TFs) orchestrating this process remain unclear. Here, by performing single-cell RNA-seq on bovine embryos, we reveal that major EGA is asynchronously initiated among blastomeres at the 8-cell stage. Integrative analyses reveal distinctive protein accumulation compared to transcription and translation activation during bovine EGA. Furthermore, we investigate the role of SP1, a TF activated at the minor EGA stage, with motifs enriched in accessible chromatin during major EGA stage in bovine and human embryos. SP1 deficiency leads to morula arrest in bovine and impairs EGA in human embryos. Multi-omics analysis demonstrates that SP1 promotes early lineage gene expression by modulating nearby chromatin states in bovine and directly targets key EGA genes in human embryos. Together, our study delineates the dynamics of bovine EGA and uncovers the conserved and species-specific roles of SP1 in regulating EGA and early development in mammals.
2026-02-12 | GSE304792 | GEO
Project description:## Overview This dataset contains mass spectrometry-based proteomics results from term placenta tissue specimens collected at birth from a cohort of pregnant individuals. The aim was to characterize placental protein expression in relation to maternal depressive symptoms and Selective Serotonin Reuptake Inhibitor (SSRI) treatment during the antenatal period. ## Project Details ### Participants and Sample Stratification Placenta tissue samples were collected from pregnant individuals in metropolitan Vancouver, Canada, as part of an ethically approved observational cohort study (University of British Columbia/Children’s and Women’s Research Ethics Board: H12-00733, H16-02280). Written informed consent was obtained from all participants, and study procedures complied with the Helsinki Declaration (2008 revision). Depressive symptoms were assessed using the Mini International Neuropsychiatric Interview (MINI) and the Hamilton Depression Rating Scale (HAM-D) at recruitment and at 36 weeks gestation. Group assignment was determined as follows: - Symptomatic depression: HAM-D score ≥ 8 at 36 weeks gestation - Control group: HAM-D < 8 and no SSRI treatment - Three groups included: (1) Controls, (2) Mild/moderate depressive symptoms without SSRI, (3) Mild/moderate depressive symptoms with SSRI Participants exposed to SSRIs (fluoxetine, paroxetine, sertraline, citalopram, or escitalopram) received treatment for at least 75 days prior to delivery, with adherence monitored throughout pregnancy. Individuals meeting exclusion criteria (medical/psychiatric conditions other than unipolar depression/anxiety, substance abuse, gestational hypertension, diabetes, placental insufficiency, fetal anomaly, intrauterine growth restriction) were not included. **The final dataset comprises 70 placenta samples
2025-12-22 | PXD071192 | Pride
Project description:<p>Cases with Type 1 Diabetes (T1D) in the UK, were part of the Wellcome Trust Case Control Consortium (WTCCC) - <a href="http://www.wtccc.org.uk" target="_blank">http://www.wtccc.org.uk</a> - that first reported in 2007:</p> <p>Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661-678. [PubMed: <a href="http://www.ncbi.nlm.nih.gov/pubmed/17554300" target="_blank">17554300</a>]</p> <p>In this genome-wide association study (GWAS), funded by the NIH and JDRF, and sponsored by the Type 1 Diabetes Genetics Consortium (T1DGC), we were able to extend the case and control groups used in the WTCCC, with the intention of performing a well-powered meta-analysis.</p> <p>The study is written up as:</p> <p>Barrett, J.C., Clayton, D.G., Concannon, P., Akolkar, B., Cooper, J.D., Erlich, H.A., Julier, C., Morahan, G., Nerup, J., Nierras, C., Plagnol, V., Pociot, F., Schuilenburg, H., Smyth, D.J., Stevens, H., Todd, J.A., Walker, N.M., Rich, S.S. and The Type 1 Diabetes Genetics Consortium Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nature Genetics, PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/19430480" target="_blank">19430480</a>.</p> <p>Resources - data:</p> <p>* Case data from this study is deposited here (i.e. in dbGaP)</p> <p>* Control data from this experiment - with subjects from the 1958 British Birth Cohort - is deposited with the European Genotype Archive (EGA):</p> <p><a href="http://www.ebi.ac.uk/ega/" target="_blank">http://www.ebi.ac.uk/ega/</a></p> <p>from where the WTCCC data is also available.</p> <p>* A complete description of how to request all components of the meta-analysis is available at:</p> <p><a href="http://www.t1dbase.org/page/PosterView/display/poster_id/324" target="_blank">http://www.t1dbase.org/page/PosterView/display/poster_id/324</a></p> <p>* Additional genetic data on the same case subjects, including some HLA types, are available from the Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory (JDRF/WT-DIL):</p> <p><a href="http://www-gene.cimr.cam.ac.uk/todd/" target="_blank">http://www-gene.cimr.cam.ac.uk/todd/</a></p> <p>Resources - samples:</p> <p>Case and control DNA samples are also available:</p> <p>* Case DNA samples are available from the JDRF/WT-DIL, as above, and will be available from the NIDDK Genetics Repository at Rutgers:</p> <p><a href="https://www.niddkrepository.org" target="_blank">https://www.niddkrepository.org</a></p> <p>* Control DNA samples are available from the 1958 British Birth Cohort (aka National Child Development Study):</p> <p><a href="http://www.cls.ioe.ac.uk/studies.asp?section=000100020003" target="_blank">http://www.cls.ioe.ac.uk/studies.asp?section=000100020003</a></p> <p>Use restrictions:</p> <p>There are access limitations to both data and samples, in order to keep their use in line with subjects' consent.</p>
| phs000180 | dbGaP
Project description:Embryonic genome activation (EGA), a pivotal transcriptional event during preimplantation development, is accompanied by post-transcriptional regulation of maternal mRNAs. Disentangling the transcriptional output of the newly activated embryonic genome from concomitant post-transcriptional processing is important for decoding EGA dynamics.Here, using optimized low-input SLAM-seq (thiol(SH)-linked alkylation for the metabolic sequencing) in mouse embryos, we delineates the temporal hierarchy of EGA nascent transcription during mouse preimplantation embryogenesis and uncovers a mechanistic link between EGA and the first lineage specification, providing new insights into the regulatory architecture of early mammalian development.
2026-01-01 | GSE297541 | GEO
Project description:Aggregate results from 43 Carbamazepine-induced hypersensitivity syndrome patients and 1296 1958 British Birth Cohort control samples
| EGAD00000000059 | EGA
Project description:Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive motor neuron loss. IsomiRs are microRNA (miRNA) isoforms that arise from alternative processing or editing events during miRNA biogenesis. While isomiRs may carry distinct biological and clinical relevance, their potential as cell-free biomarkers in neurodegeneration remains largely unexplored. Here we investigated the prognostic utility of plasma isomiRs in ALS, using next-generation sequencing. We profiled cell-free isomiRs in 154 ALS patients from a British cohort and identified higher levels of one isomiR, let-7g-5p.t, to be associated with longer survival. This finding was independently validated in an international ALS cohort of 200 patients and was in two orthogonal approaches. let-7g-5p.t prognostic utility was comparable to that of neurofilament light chain (NfL) or miR-181. These results establish isomiRs as a novel class of blood-based biomarkers in ALS with potential to refine prognostication in clinical trials for neurodegenerative diseases.
2025-10-31 | GSE298532 | GEO