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single cell Bisulfite-seq

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https://www.readbyqxmd.com/read/27895806/genome-wide-epigenomic-profiling-for-biomarker-discovery
#1
REVIEW
René A M Dirks, Hendrik G Stunnenberg, Hendrik Marks
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27848892/single-cell-sequencing-for-drug-discovery-and-drug-development
#2
Hongjin Wu, Charles Wang, Shixiu Wu
Next-generation sequencing (NGS), particularly single-cell sequencing, has revolutionized the scale and scope of genomic and biomedical research. Recent technological advances in NGS and single-cell studies have made the deep whole-genome (DNA-seq), whole epigenome and whole-transcriptome sequencing (RNA-seq) at single-cell level feasible. NGS at the single-cell level expands our view of genome, epigenome and transcriptome and allows the genome, epigenome and transcriptome of any organism to be explored without a priori assumptions and with unprecedented throughput...
November 16, 2016: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/27718505/optimization-of-techniques-for-multiple-platform-testing-in-small-precious-samples-such-as-human-chorionic-villus-sampling
#3
Margareta D Pisarska, Marzieh Akhlaghpour, Bora Lee, Gillian M Barlow, Ning Xu, Erica T Wang, Aaron J Mackey, Charles R Farber, Stephen S Rich, Jerome I Rotter, Yii-der I Chen, Mark O Goodarzi, Seth Guller, John Williams
BACKGROUND: Multiple testing to understand global changes in gene expression based on genetic and epigenetic modifications is evolving. Chorionic villi, obtained for prenatal testing, is limited, but can be used to understand ongoing human pregnancies. However, optimal storage, processing and utilization of CVS for multiple platform testing have not been established. RESULTS: Leftover CVS samples were flash-frozen or preserved in RNAlater. Modifications to standard isolation kits were performed to isolate quality DNA and RNA from samples as small as 2-5 mg...
November 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27172195/histone-h1-limits-dna-methylation-in-neurospora-crassa
#4
Michael Seymour, Lexiang Ji, Alex M Santos, Masayuki Kamei, Takahiko Sasaki, Evelina Y Basenko, Robert J Schmitz, Xiaoyu Zhang, Zachary A Lewis
Histone H1 variants, known as linker histones, are essential chromatin components in higher eukaryotes, yet compared to the core histones relatively little is known about their in vivo functions. The filamentous fungus Neurospora crassa encodes a single H1 protein that is not essential for viability. To investigate the role of N. crassa H1, we constructed a functional FLAG-tagged H1 fusion protein and performed genomic and molecular analyses. Cell fractionation experiments showed that H1-3XFLAG is a chromatin binding protein...
2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/26843056/pcr-techniques-in-characterizing-dna-methylation
#5
Khalida Wani, Kenneth D Aldape
DNA methylation was the first epigenetic mark to be discovered, involving the addition of a methyl group to the 5' position of cytosine by DNA methyltransferases, and can be inherited through cell division. DNA methylation plays an important role in normal human development and is associated with the regulation of gene expression, tumorigenesis, and other genetic and epigenetic diseases. Differential methylation is now known to play a central role in the development and outcome of most if not all human malignancies...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/22120008/regions-of-focal-dna-hypermethylation-and-long-range-hypomethylation-in-colorectal-cancer-coincide-with-nuclear-lamina-associated-domains
#6
Benjamin P Berman, Daniel J Weisenberger, Joseph F Aman, Toshinori Hinoue, Zachary Ramjan, Yaping Liu, Houtan Noushmehr, Christopher P E Lange, Cornelis M van Dijk, Rob A E M Tollenaar, David Van Den Berg, Peter W Laird
Extensive changes in DNA methylation are common in cancer and may contribute to oncogenesis through transcriptional silencing of tumor-suppressor genes. Genome-scale studies have yielded important insights into these changes but have focused on CpG islands or gene promoters. We used whole-genome bisulfite sequencing (bisulfite-seq) to comprehensively profile a primary human colorectal tumor and adjacent normal colon tissue at single-basepair resolution. Regions of focal hypermethylation in the tumor were located primarily at CpG islands and were concentrated within regions of long-range (>100 kb) hypomethylation...
January 2012: Nature Genetics
https://www.readbyqxmd.com/read/21493656/bismark-a-flexible-aligner-and-methylation-caller-for-bisulfite-seq-applications
#7
Felix Krueger, Simon R Andrews
SUMMARY: A combination of bisulfite treatment of DNA and high-throughput sequencing (BS-Seq) can capture a snapshot of a cell's epigenomic state by revealing its genome-wide cytosine methylation at single base resolution. Bismark is a flexible tool for the time-efficient analysis of BS-Seq data which performs both read mapping and methylation calling in a single convenient step. Its output discriminates between cytosines in CpG, CHG and CHH context and enables bench scientists to visualize and interpret their methylation data soon after the sequencing run is completed...
June 1, 2011: Bioinformatics
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