Bulked DNA
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Ebook "Biophysics of DNA-protein interactions: From single molecules to biological systems" would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists.
354p ladongphongthanh1008 22-04-2024 8 2 Download
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Cell-free tumor-derived DNA (ctDNA) allows non-invasive monitoring of cancers, but its utility in renal cell cancer (RCC) has not been established. Methods: Here, a combination of untargeted and targeted sequencing methods, applied to two independent cohorts of patients (n = 91) with various renal tumor subtypes, were used to determine ctDNA content in plasma and urine.
17p vibransone 28-03-2024 4 2 Download
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Accurate lung cancer classification is crucial to guide therapeutic decisions. However, histological subtyping by pathologists requires tumor tissue—a necessity that is often intrinsically associated with procedural difficulties. The analysis of circulating tumor DNA present in minimal-invasive blood samples, referred to as liquid biopsies, could therefore emerge as an attractive alternative.
12p vibransone 28-03-2024 6 2 Download
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Large numbers of autosomal sites are found differentially methylated in the aging genome. Due to analytical difficulties in dealing with sex differences in X-chromosome content and X-inactivation (XCI) in females, this has not been explored for the X chromosome.
13p vibransone 28-03-2024 1 1 Download
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In this study, we characterised the evolutionary pattern of metastatic CRC (mCRC) by analysing bulk and single-cell exome sequencing data of primary and metastatic tumours from 7 CRC patients with liver metastases. Here, 7 CRC patients were analysed by bulk whole-exome sequencing (WES); 4 of these were also analysed using single-cell sequencing.
14p vibransone 28-03-2024 6 2 Download
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Roughly 50% of adult gliomas harbor isocitrate dehydrogenase (IDH) mutations. According to the 2021 WHO classifcation guideline, these gliomas are diagnosed as astrocytomas, harboring no 1p19q co-deletion, or oligodendrogliomas, harboring 1p19q co-deletion.
19p vicwell 29-02-2024 3 1 Download
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Variation in cell composition can dramatically impact analyses in bulk tissue samples. A commonly employed approach to mitigate this issue is to adjust statistical models using estimates of cell abundance derived directly from omics data.
14p vicwell 29-02-2024 3 1 Download
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The soil borne, obligate biotrophic fungus Synchytrium endobioticum causes tumor-like tissue proliferation (wart) in potato tubers and thereby considerable crop damage. Chemical control is not effective and unfriendly to the environment. S. endobioticum is therefore a quarantined pathogen. The emergence of new pathotypes of the fungus aggravate this agricultural problem.
16p vinarcissa 21-03-2023 5 1 Download
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Production and consumption of pomegranate have been increasing in the world in recent years due to its health benefits to humans. Sunburn is an important physiological disorder caused by high temperature, light, and radiation. With the changes in climatic conditions that have occurred in recent years, the effect of sunburn is increasing and limiting the production and quality of pomegranate.
14p lyhuyenthu 31-01-2023 10 2 Download
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Alternative splicing is a key regulatory mechanism in eukaryotic cells and increases the effective number of functionally distinct gene products. Using bulk RNA sequencing, splicing variation has been studied across human tissues and in genetically diverse populations.
14p vigalileogalilei 27-02-2022 8 1 Download
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We describe a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts or genomic regions from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, which are all pre-selected and optimized in silico.
16p vielonmusk 30-01-2022 21 0 Download
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Cell type heterogeneity presents a challenge to the interpretation of epigenome data, compounded by the difficulty in generating reliable single-cell DNA methylomes for large numbers of cells and samples. We present EPISCORE, a computational algorithm that performs virtual microdissection of bulk tissue DNA methylation data at single cell-type resolution for any solid tissue.
33p viarchimedes 26-01-2022 9 0 Download
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Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Here we describe a computational strategy to reliably determine complete whole-chromosome haplotypes using a combination of bulk long-range sequencing and Hi-C sequencing.
31p viarchimedes 26-01-2022 12 0 Download
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The traditional approach to studying the epigenetic mechanism CpG methylation in tissue samples is to identify regions of concordant differential methylation spanning multiple CpG sites (differentially methylated regions).
23p viarchimedes 26-01-2022 10 0 Download
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Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution. Continuing drops in sequencing costs are beginning to enable high-throughput surveys of DNA methylation in large samples of individuals and/or single cells.
8p vijeeni2711 24-07-2021 5 0 Download
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Certain sequences of genomic mutations can lead to cancer formation and affect treatment outcomes and drug resistance. We constructed a cancer evolutionary tree using bulk-targeted deep sequencing to explore the impact of sequential and co-occurring somatic mutations on patients with stage III colorectal cancer (CRC).
11p vianrose2711 27-04-2021 9 1 Download
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The large-scale availability of whole-genome sequencing profile from bulk DNA sequencing of cancer tissues is fueling the application of evolutionary theory to cancer.
11p vikentucky2711 24-11-2020 10 1 Download
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With the advent of array-based techniques to measure methylation levels in primary tumor samples, systematic investigations of methylomes have widely been performed on a large number of tumor entities. Most of these approaches are not based on measuring individual cell methylation but rather the bulk tumor sample DNA, which contains a mixture of tumor cells, infiltrating immune cells and other stromal components.
9p vicolorado2711 23-10-2020 12 1 Download
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Standard RNAseq methods using bulk RNA and recent single-cell RNAseq methods use DNA barcodes to identify samples and cells, and the barcoded cDNAs are pooled into a library pool before high throughput sequencing. In cases of single-cell and low-input RNAseq methods, the library is further amplified by PCR after the pooling.
9p vicolorado2711 23-10-2020 11 0 Download
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Recently, it has become possible to collect next-generation DNA sequencing data sets that are composed of multiple samples from multiple biological units where each of these samples may be from a single cell or bulk tissue.
10p vicolorado2711 22-10-2020 15 1 Download