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ChIP-seq analysis
Published in Altuna Akalin, Computational Genomics with R, 2020
There are four steps in ChIP quality control: Sample correlation clustering: Clustering of the pair-wise correlations between genome-wide signal profiles.Data visualization in a genomic browser.Average fragment length determination: Determining whether the ChIP was enriched for fragments of a certain length.Visualization of GC bias. Here we will plot the ChIP enrichment versus the average GC content in the corresponding genomic bin.
Gas Chromatographic Analysis
Published in Adorjan Aszalos, Modern Analysis of Antibiotics, 2020
As mentioned, two of the parameters of GC that can be varied to develop useful chromatographs are temperature and column material. When a specific pharmaceutical ingredient, or a simple mixture of similar materials, is being analyzed, a method involving a column and a specific temperature (isothermal) often works quite well. However, the need sometimes arises to analyze complex mixtures. It is impractical to change the column material during the course of analysis; however, the column temperature can be changed readily. Many of the commercial instruments are intended to be used with temperature programming. The usual approach is to first chromatograph at a low temperature so that the more volatile analytes are discernible and analyzable without being part of the solvent front. Then the column temperature is raised according to a preset program to the point at which the least volatile analytes of interest chromatograph within a reasonable time. Often, at the end of the analysis, the instrument is programmed to return to the initial temperature automatically. Obviously, by temperature programming, many analyses are accomplished that would otherwise be impossible.
Homology of Nonrepeated DNA Sequences in Phylogeny of Fungal Species
Published in S. K. Dutta, DNA Systematics, 2019
The GC (guanine + cytosine) mol% of DNA has been used to identify the affinities between a wide range of bacteria, lower eukaryotes, higher plants, and animals. In fungi, Storck and Alexopoulos7 and Storck8 have reviewed the GC mol% and concluded on the basis of available information that zygomycetes on the average have the lowest GC content and the basidiomycetes the highest (the ascomycetes falling between these two groups). The GC content of hemiascomycetes varies from 29 to 50% and is closer to that of zygomycetes, whereas the euascomycetes have a range of 50 to 60% and are closer to the heterobasidiomycetes. The percent GC content of most deuteromycetes is close to that for ascomycetes.
Site-specialization of human oral Gemella species
Published in Journal of Oral Microbiology, 2023
Julian Torres-Morales, Jessica L. Mark Welch, Floyd E. Dewhirst, Gary G. Borisy
A recent study evaluated the acquisition of proteins by horizontal transfer in the genus Gemella and concluded that genes encoding proteins core to a single species, but not to the whole genus, tended to have an unusual GC content [35]. We therefore evaluated the GC content of the RibBA, RibD, RibH, and RibE genes, which form a single operon. We found no significant difference in GC% of these genes compared to all genes in G. haemolysans genomes (32.9% ± 1.9% and 31.5% ± 5.5%, respectively). A BLAST search showed no significant similarity to any other bacterial taxon, although it did reveal high similarity (E-value = 2.5E−158 with 99% coverage on average) of two genes to a partial virus assembly from human metagenomes. While this finding is suggestive, it leaves the source of the operon as an open question.
Epigenetic signatures in gastric cancer: current knowledge and future perspectives
Published in Expert Review of Molecular Diagnostics, 2022
Fatma Sogutlu, Mert Pekerbas, Cigir Biray Avci
In conclusion, epigenetic alterations are common in GC as well as in other types of cancer. In addition, some histopathological and molecular subtypes of GC are closely related to factors such as dietary habits and microorganisms, regardless of distinctive genetic predisposition. It is also interesting that certain molecular subtypes introduced by TCGA in 2014 overlap with the epigenetic classes defined by Matsukaka et al. [9]. This overlap supports that genetic and epigenetic aberrations may originate from common factors. Epigenetic alterations revealed to date in GC usually occur at the level of methylation, histone modifications, and non-coding RNA. To date, many studies revealed that changes in the methylation patterns in specific genes or at the genome level are common in GC. Specific histone modifications and changes in the expression level of genes involved in histone modifications (HATs, HDACs, HMTs, and HDMs) are closely associated with gastric cancer. Differences are also observed in the expression levels of non-coding RNAs, and these RNAs are involved in many processes in GC, such as cell proliferation, apoptosis, EMT, and metastasis. Considering that these changes can be detected long before GC can be detected histopathologically, they have great potential as early diagnosis and treatment targets and are expected to become the focus of molecular studies on gastric cancer.
Diagnostic profile of the AmplideX Fragile X Dx and Carrier Screen Kit for diagnosis and screening of fragile X syndrome and other FMR1-related disorders
Published in Expert Review of Molecular Diagnostics, 2021
Elizabeth Berry-Kravis, Lili Zhou, Jonathan Jackson, Flora Tassone
The workflow for the test includes PCR Master Mix setup, thermal cycling, and analysis using CE. A specimen (purified gDNA) or control (Diluent or Fragile X Positive Control) is added to a PCR reaction well containing a Master Mix with the GC-Rich Amp Buffer, GC-Rich Polymerase Mix, Fragile X Primer Mix for a total of 15 μL. These proprietary reagents constitute a set of PCR reagents that enable highly efficient amplification of GC-rich DNA based on innovations in 3 areas: (a) the gene-specific primers, (b) the amplification buffer for GC-rich templates, and (c) the PCR cycling conditions. The primers were selected after screening of >60 distinct primer pairs to identify the optimal pair. More than 1000 different combinations of PCR additives and other buffer components were evaluated with model DNA templates to identify conditions that depressed the amplicon melting temperature (Tm) while still supporting primer binding and efficient PCR amplification. Promising combinations of primers and buffer were then iteratively evaluated with various PCR conditions to generate the final reagent set and procedures [11]. After thermal cycling, unpurified PCR products are directly mixed with Hi-Di™ Formamide and ROX 1000 Size Ladder. Following denaturation, amplicons are resolved on an Applied Biosystems™ 3500 Dx Genetic Analyzer running POP-7™ polymer and analyzed using the AmplideX Fragile X Reporter. Figure 3 displays a schematic of the workflow.