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DNA extraction

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Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing

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Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read. Here we report a DNA extraction protocol that is optimized for long-read WGS of NTM, yielding large quantities of highly pure DNA with no additional clean-up steps..

Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples

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The paired benign breast disease fresh frozen samples under- went DNA extraction using QIAGEN’s Gentra Puregene Kit following manufacturer ’ s guidelines for DNA Purifi- cation from Tissue.

A toolkit for studying Varroa genomics and transcriptomics: Preservation, extraction, and sequencing library preparation

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Each treatment group was subjected to DNA and RNA extractions at intervals of and 21 days for subsequent DNA and RNA quantity and quality evaluations. By visual inspection, ground mite powder that remained on the pestle was used for DNA extraction, ensuring that about half of the mite homogenates re- main in the tubes for RNA extraction (Fig. Mite DNA was extracted using a QIAamp DNA Micro kit (Qiagen, Tokyo, Japan), according to the manufac- turer’s protocol.

Analysis of the fecal microbiota of fast- and slow-growing rainbow trout (Oncorhynchus mykiss)

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In this study, the DNA extraction methodology comparison was performed to optimize the extraction methodology and apply this to the comparison of fast- and slow-growing fish gut microbiota. The effects of the DNA extraction methods were assessed on the basis of the DNA quantity, quality and the inter-sample variation in microbial communities between replicates. The concentration and the quality of the DNA.

Molecular Biology Problem Solver 57

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Laboratory measurements, with pH meters, 90. spectrophotometers, 95–96 Linear acrylamide, in RNA. in DNA extraction in gene expression, 479–480 in plasmid purification, 180–182 in RNA purification, 215 of yeast cells, 209 Lysis buffers. in DNA extraction, 173 in DNA purification, 169 Lysozyme, cell disruption via, 217,. in DNA extraction, 173 in DNA purification, 169 Media preparation facilities, 132 Media preparation staff, 132–133 Media room, labware sterilization in,. See also Dry.

DNA methylation profiles correlated to striped bass sperm fertility

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Aliquots of striped bass semen were collected at the time of spawning for DNA extraction and sequencing and snap frozen in liquid ni- trogen. Briefly, approximately 1 mL of semen was put into a sterile conical tube and was then subsequently di- luted with isosmotic (350 mOsmol/Kg) Striped Bass Extender [20] to provide an extended striped bass semen mixture containing approximately one billion sperm cells per 100 μL of extended semen.

Fungal DNA barcode (ITS nrDNA) reveals more diversity than expected in Tulostoma from Macedonia

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Molecular analysis based on the internal transcribed spacers (ITS) of nuclear ribosomal DNA (nrDNA), accepted as the DNA barcode for fungi (Schoch et al., 2012), provides valuable information for species identification.. Recently, Jeppson et al. DNA extraction, amplification, and sequencing of the ITS regions including the 5.8S of the ribosomal RNA gene cluster followed the protocols mentioned by Phosri et al..

Molecular Biology Problem Solver 58

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DNA contamination with, 169 in DNA extraction, 173. in RNA purification . Sales representatives, 14–18 expectations of, 15–16 functions of, 15 leverage via, 17–18 motivations of, 16 for pH meters, 94 relating to, 16–17. in DNA precipitation . See also DNA. as affecting balance accuracy, 55 with pH meters, 93–94. in Western blotting, 382–383 Sample location, as affecting balance.

Genetically modified roundup ready soybean in processed meat products in the Kingdom of Saudi Arabia

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DNA from some sausages samples, lanes 9 and 10: DNA from some mortadella samples, lane 11: PCR product from some luncheon chicken, lane 12: marker provide with GMOScreen kits.. that the DNA extraction method used in this study allowed the extraction of amplifiable soybean DNA from meat samples.. The obtained results demon- strated the presence of Roundup Ready soybean in the commercial processed meat products in Kingdom of Saudi Arabia.

Khóa luận tốt nghiệp đại học: Nghiên cứu tình trạng methyl hoá chỉ thị phân tử SEPT9 ở bệnh nhân ung thư đại trực tràng Việt Nam

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Tách chiết DNA từ mẫu mô cố định formaldehyde bằng phương pháp sử dụng bộ KIT Tissue Genomic DNA Extraction Mini Kit cho ra 5 mẫu có tỷ số OD 260/230 dưới 1,6 (chiếm 62,5. Phương pháp Tỷ lệ. đối với phương pháp B. Nội dung Phương pháp. Đường chạy số 1: Sản phẩm DNA được tách chiết bằng phương pháp B 16 chưa tối ưu (nồng độ DNA : 150 ng/µl). Đường chạy số 1: Sản phẩm DNA được tách chiết bằng phương pháp B 16 đã tối ưu (nồng độ DNA: 936 ng/µl).

DNA barcoding of black cherry aphid Myzus cerasi (Fabricus, 1775) (Hemiptera: Aphididae) populations collected from Prunus avium and Prunus cerasus

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After DNA extraction from a single aphid, partial sequences of the COI gene was amplified with either CO-I forward primer 5’- TCTTCTCTTTACATTTAGCAGGAAT-3’ or CO-I reverse primer 5’-AATAGATGAATTAGCAAGAATTA-3’. (Turcinaviciene et al., 2006). and a final extension for 5 min (1 cycle) (Rakauskas et al., 2014). Black cherry aphid colonies on the terminal growth of host plant (Denizli, Honaz)..

Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants

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Notably, previous studies examining the gut microbiota using 16S rRNA gene sequencing in infants have highlighted that the DNA extraction method, and the annealing efficiency of the primers used for the amplification step, can significantly impact the representative bacterial profile obtained [13].

Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

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In the last decade, together with more refined DNA extraction and laboratory methods tailored to efficiently retrieve very short and scarce DNA sequences [5, 11], it has become possible to obtain massive amounts of se- quences from ancient material using high-throughput sequencing technologies.

Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing

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The mantle tissues of the left valves were sampled for DNA extraction. 5 Relative expression levels of shell colour-related genes in the mantle tissues of Yesso scallops with different shell colours. methylation, scallops with the same sex (male) were chosen in the present study. Conversions of C to T and G to A were separately made in the reference genome and se- quence reads before alignment, and the bisulfite- converted genome was indexed by Bowtie2 [68].

Rapid sex determination of preimplantation bovine embryo using direct-PCR from a single blastomere

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As showed in Figure 2, male genomic DNA amplifications were successful on BY marker with 300 bp product, without any consid- erable non-specific amplified products. Enhance sensitivity of sex determination of bovine embryo using direct PCR from single embryonic blastomere.. For that reason, we excluded the DNA extraction step out of the sex- ing process, which introduces the risk of loss of DNA material.

Identification of bacteroides spp. from ducks using 16s RRNA gene PCR assay: Prelude to its application in microbial source tracking

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Of the 50, 20 were subjected to total DNA extraction and the remaining 30 were used for the isolation of Bacteroides. This shows an intraspecies difference between Bacteroides species in the Philippines and Japan. This difference is a result of variations in the gut microbiome such as host species, diet, and geography.

Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array

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For MoBa-START, 500 nanograms of DNA stored in the MoBa Biobank (see Paltiel et al. Further details of the DNA extraction and quality control process of EPIPREG can be found in Supplementary File 3.. Chronological age in days was regressed on 770,586 autosomal CpGs that remained after quality control. The mixing parameter (alpha) was set to 0.5 and the shrinkage parameter (lambda) leading to the minimum mean square error was selected after 10- fold cross-validation in the training set.

DNA methylation in infants with low and high body fatness

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DNA extraction and DNA methylation analysis. 500 ng of genomic DNA was bisulfate converted with EZ-96 DNA Methylation kit (Zymo Research, Irvine, CA, USA) and genome wide DNA methylation analysis was per- formed using the Infinium Human Methylation 450 K BeadChip (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.. Illumina 450 K DNA methylation data was pre- processed using functional normalization [52] as imple- mented in minfi [53].

Epigenetic analysis of high and low motile sperm populations reveals methylation variation in satellite regions within the pericentromeric position and in genes functionally related to sperm DNA organization and maintenance in Bos taurus

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DNA extraction, library preparation and sequencing Four HM and four LM sperm samples obtained in previ- ous step were used for DNA extraction. The General Linear Model procedure (PROC GLM) was used to evaluate the efficiency of the sperm separation comparing semen qual- ity parameters at thawing and in the HM population. The model included the fixed effect of the sperm population, and bull as random. Data are available in the Sequence Reads Archive (SRA), (Accession Number SRP119411)..

Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples

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Fur- ther NGS analysis results placed the extraction kits in the order of decreasing extraction efficiency as follows:. RNA extraction kits were also applicable for metage- nomic analysis of the DNA virus, probably by effectively capturing the RNA transcripts of the DNA virus in the extracted clinical sample..