Ontology highlight
ABSTRACT:
PROVIDER: PRJNA291336 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Effect of DNA extraction method on brain DNA copy number estimation
| PRJNA291022 | ENA
Project description:Copy number mosaicism in the human brain has been reported recently by several authors. This experiment was performed to further investigate our preliminary data of apparent widespread deletions in brain DNA, detected in a custom Agilent aCGH designed for Parkinson's disease (PD) genes in both patients and controls, and supported by droplet digital PCR. To avoid any effect of diseased tissue, we used only controls here. All DNA was freshly extracted. A validated SNP array was chosen to ensure that our results were not due to artefacts specific to the aCGH design used, with SNP array giving the additional advantage of B allele frequency estimation.
2016-02-01 | GSE71429 | GEO
Project description:A preliminary understanding of the phenotypic effect of copy number variation (CNV) of DNA segments is emerging. These rearrangements were demonstrated to influence, in a somewhat dose-dependent manner, the expression of genes mapping within. They were shown to also affect the expression of genes located on their flanks, sometimes at great distance. Here, we show by monitoring these effects at multiple life stages, that these controls over expression are effective throughout mouse development. Similarly, we observe that the more specific spatial expression patterns of CNV genes are maintained throughout life. However, we find that some brain-expressed genes appear to be under compensatory loops only at specific time-points, indicating that the influence of CNVs on these genes is modulated through development. We also observe that CNV genes are significantly enriched upon transcripts that show variable time-course of expression in different strains. Thus modifying the number of copy of a gene not only potentially alters its expression level, but possibly also its time of expression. Keywords: comparative genomic Expression from brain and liver tissues from C57BL/6J, DBA2/J and 129S2 mouse strains at different developmental time points.
2010-11-17 | E-GEOD-16675 | biostudies-arrayexpress
Project description:Copy number variants (CNVs) affect both disease and normal phenotypic variation but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrate accurate estimation of absolute copy number for duplications as small as 1.9 kbp, ranging from 0-48 copies. We identified 4.1 million ‘singly unique nucleotide’ (SUN) positions informative in distinguishing specific copies, and use them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.
2010-09-24 | GSE24334 | GEO
Project description:Array-based comparative genomic hybridisation is a high-resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide libraries for array CGH. This oligo array CGH platform yields reproducible results and is capable of detecting single copy gains, multi-copy amplifications as well as homozygous and heterozygous deletions as small as 100 kb with high resolution. A human oligonucleotide library was printed on amine binding slides. Arrays were hybridised using a hybstation and analysed using BleuFuse feature extraction software, with over 95% of spots passing quality control. The protocol allows as little as 300 ng of input DNA without the need for amplification or target reduction and a 90% reduction of Cot1-DNA without compromising quality. High quality results have also been obtained with DNA from archival tissue. Finally, in addition to human oligo arrays, we have applied the protocol successfully to mouse oligo arrays. We believe that this oligo-based platform using “off-the-shelf” oligo-libraries provides an easy accessible alternative to BAC arrays for CGH, which is cost-effective, available at high resolution and easily implemented for any sequenced organism without compromising the quality of the results. Keywords: comparative genomic hybridization, oligonucleotide,
2005-12-19 | GSE3264 | GEO
Project description:Human lung adenocarcinoma DNA copy number profiling
| PRJNA155569 | ENA
Project description:To address how genetic variation alters gene expression in complex cell mixtures, we developed Direct Nuclear Tagmentation and RNA-sequencing (DNTR-seq), which enables whole genome and mRNA sequencing jointly in single cells. DNTR-seq readily identified minor subclones within leukemia patients. In a large-scale DNA damage screen, DNTR-seq was used to detect regions under purifying selection, and identified genes where mRNA abundance was resistant to copy number alteration, suggesting strong genetic compensation. mRNA-seq quality equals RNA-only methods, and the low positional bias of genomic libraries allowed detection of sub-megabase aberrations at ultra-low coverage. Each cell library is individually addressable and can be re-sequenced at increased depth, allowing multi-tiered study designs. Additionally, the direct tagmentation protocol enables coverage-independent estimation of ploidy, which can be used to identify cell singlets. Thus, DNTR-seq directly links each cell?s state to its corresponding genome at scale, enabling routine analysis of heterogeneous tumors and other complex tissues.
2020-10-22 | GSE144296 | GEO