Enancher_8x60K
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010001153 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:It is becoming clear that copy number polymorphism in the human genome is a significant form of genetic variation. We have developed a new method that uses SNP genotype data from parent-offspring trios and applied it to HapMap to conduct high-resolution detection of deletion polymorphism. Of the delections uncovered, approximately 100 have been experimentally validated using comparative genome hybridization on these tiling-resolution oligonucleotide microarrays. We identified a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the parent-offspring trios. This new method will permit future identification of deletion polymorphisms from high density SNP data derived from parent-offspring trios or other family relationships. Keywords: comparative genomic hybridisation
2005-11-17 | GSE3474 | GEO
Project description:Intellectual disability is a common condition that carries lifelong severe medical and developmental consequences. The causes of intellectual disability (ID) remain unknown for the majority of patients due to the extensive clinical and genetic heterogeneity of this disorder. De novo mutations may play an important role in ID as most individuals with ID present as isolated cases without family history and/or clear syndromic indication. In addition, the involvement of such mutations have recently been demonstrated in a small number of individuals with ID. Here we evaluate the diagnostic potential and role of de novo mutations in a cohort of 100 patients with ID of unknown cause using family-based exome sequencing. Single end short-read (50 bp) SOLiD 4 sequencing data for 300 individuals, constituting 100 patient-parent trios. For more details please read; http://www.nejm.org/doi/full/10.1056/NEJMoa1206524. Dataset is created by RUNMC (Radboud University, Nijmegen Medical Center), partner of Geuvadis consortium (http://www.geuvadis.org).
2013-11-06 | E-GEUV-5 | 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:The paired box gene 6 (PAX6) is an essential transcription factor for eye formation. Genetic alterations in PAX6 can lead to various ocular malformations including aniridia. The purpose of this study was to identify genetic defects as the underlying cause of familial coloboma of iris in a large Chinese family. After linkage analysis was carried out in this family, all exons of PAX6 in the proband were sequenced by the Sanger sequencing technique. Then the genome of the proband was evaluated by a microarray-based comparative genomic hybridization (aCGH). Quantitative real-time PCR was applied to verify the abnormal aCGH findings. All patients presented bilateral partial coloboma of iris, severe congenital nystagmus, hyperpresbyopia and congenital posterior polar cataracts. Two-point linkage analysis in the autosomal dominant family showed loss of heterozygosity at the D11S914 locus. There was no pathogenic mutation in the exons of PAX6. The aCGH analysis revealed a 681 kb heterozygous deletion on chromosome 11p13. Quantitative real-time PCR verified the deletion in the patients and further confirmed this deletion cosegregation with the coloboma of iris phenotype in the family. The 681 kb large deletion of chromosome 11p13 downstream of PAX6 is the genetic cause of the familial coloboma of ocular in this large Chinese family. aCGH should be applied if there is a negative result for the mutation detection of PAX6 in patients with aniridia.
2013-09-05 | GSE50577 | GEO
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:ChIP-seq experiment of 14 human lymphoblastoid cell line samples from the 1000 Genomes sample set (http://www.1000genomes.org/). Dataset includes two parent-daughter trios (CEU and YRI populations) and additional eight unrelated individuals (CEU population). This accession contains raw and mapped ChIP-seq read data, other assays in this study are available under accession E-MTAB-1883 (RNA-seq, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1883) and E-MTAB-1885 (GRO-seq, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1885/).
2013-10-17 | E-MTAB-1884 | biostudies-arrayexpress
Project description:This single cell RNA-seq experiment was performed to quantify DLL3 expression in tumor cells in small cell lung cancer patients.Tumors were rapidly dissociated after the surgical procedure using the Miltenyi Biotec Human Tumor Dissociation kit (cat# 130-095-929). Libraries were constructed using the VDJ NextGEM v1.1 10x Genomics Chromium kit according to the manufacturer's instructions. Samples were sequenced on a NextSeq 550 sequencer (Illumina). Corresponding EGA study number: EGAS50000001400, EGA dataset number: EGAD50000002034.
2025-12-11 | E-MTAB-16412 | biostudies-arrayexpress
Project description:Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents were tested using Illumina SNP arrays to find new imprinted genes to ascertain the extent of allele specific expression in this tissue.
2010-04-15 | E-TABM-796 | biostudies-arrayexpress