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RNA extraction

Tìm thấy 15+ kết quả cho từ khóa "RNA extraction"

A comparison of RNA extraction and sequencing protocols for detection of small RNAs in plasma

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Differentially detected miRNAs between RNA extraction/.

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..

Comparison of RNA isolation methods on RNA-Seq: Implications for differential expression and meta-analyses

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Sultan and colleagues compared two RNA isolation methods (Qiagen RNeasy kit and guanidinium-phenol (TRIzol) extraction) and two library selection schemes (poly-A enrichment and rRNA depletion) on downstream transcript abundance estimates, and found that rRNA depletion was particu- larly sensitive to the RNA extraction method [2].

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.

RNA-QC-chain: Comprehensive and fast quality control for RNA-Seq data

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In extracted total RNA, up to 80–90% are rRNA sequences, thus a high quality RNA-Seq experiment requires an intact total RNA extraction and efficient. 2 Selected outputs of RNA-QC-Chain for a RNA-Seq data of Nannochloropsis (Dataset 1). In Dataset 2, we artificially added some yeast data as external contaminations but are not aware in advance that bacteria reads were also included in the downloaded rat RNA-Seq data.

A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples

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The quality of the RNA samples from the fifteen clinical samples. Comparison of four RNA library preparation kits for FFPE samples. The consistency of transcript quantification of four RNA library preparation kits with FFPE samples. Comparison of mapping data using HISAT and STAR in FF and FFPE samples. RNA-seq: RNA sequencing. Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples.

The micro-RNA content of unsorted cryopreserved bovine sperm and its relation to the fertility of sperm after sexsorting

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EK performed the lab work (total RNA extraction and quality control, preparation of small RNA libraries), carried out part of the bioinformatic analysis, reviewed the existing literature and prepared the manuscript. SiB carried out part of the lab work (total RNA extraction and quality control, preparation of small RNA libraries). SW and UW contributed to the conception of the work, the collection of the samples and fertility data.

Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes

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Given the import- ance obtaining sufficient amounts of high quality RNA for expression studies, we optimized RNA extraction from FACS sorted cells from zebrafish embryos and did an in-depth quality assessment of the extracted RNA, the latter often omitted in performed experiments.

Exploring the unmapped DNA and RNA reads in a songbird genome

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DNA was extracted from whole blood of the reference bird and sequenced with Illumina HiSeq 2000 at ~ 95X. 4 Schematic overview of the workflow used for the analysis of unmapped reads of DNA and RNA datasets. of the reference bird where the majority of the RNA comes from the nucleated red blood cells. Blood RNA extraction was done with Direct-zol RNA miniPrep Plus kit (Zymo Research) with a modification in the start of the protocol. Mapping and alignment of the DNA reads.

Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion

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Finally, EMBR-seq effectively captures the transcriptome from 500-fold lower starting total RNA compared to commercial kits, thereby providing a powerful new ap- proach to investigate gene expression patterns in rare and non-cultivable bacterial species.. The cells were stored on ice and total RNA extraction was performed immediately.. EMBR-seq Poly adenylation.

Expression analysis of lung miRNAs responding to ovine VM virus infection by RNA-seq

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The figure illustrates the four steps of the data analysis starting from the RNA extraction and sequencing: miRNA detection and prediction, differential expression, target prediction and functional analysis. We built three sets of genes that interacted in our predictions with any of the DE miRNAs in each comparison. The U6 snRNA, oar-miR-30d and oar-miR-191 were tested as in- ternal standard controls and the last two were selected for their expression stability in our samples.

Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots

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The tis- sue samples were first ground in liquid nitrogen, and 100 mg of the tissue was aliquoted for RNA extraction.. processed following the remaining steps of the Qiagen RNeasy Plant Mini Kit’s instructions.. Differential expression analysis was conducted using the DeSeq2 1.16.1 pipeline which normalizes libraries based on the geometric mean of the read counts and then calcu- lates the log 2 fold change between a defined ‘experimental’.

Environmental RNAi pathways in the twospotted spider mite

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Column enrichment of small RNA containing complexes used 1 mL HiTrap Q FF columns (GE Lifesciences) as previously described [20]. RNA obtained from both column extraction and total RNA extraction were sequenced from an Illumina True- Seq Small RNA Library Prep Kit library. Small RNA TruSeq libraries were initially processed using Fastx toolkit to remove adapter sequences [33].

Acting locally - affecting globally: RNA sequencing of gilthead sea bream with a mild Sparicotyle chrysophrii infection reveals effects on apoptosis, immune and hypoxia related genes

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González from IATS, for technical assistance with RNA extraction and gene expression analyses, and Slavica Colak, DVM, for her valuable help in planning, organizing and managing fish sampling at the aquaculture facility in the Adriatic Sea.. These funding bodies had no role in the design of the study, collection, analysis, and interpretation of data, or in writing the manuscript. All data generated by this study are included in the article and its additional files.

Các phương pháp phát hiện virus gây bệnh cho lan

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RNA tổng số được tách chiết từ mô lá của mẫu Lan nghi ngờ và 1 mẫu thực vật làm đối chứng theo hướng dẫn kit tách chiết (ở đây tôi trình bày tóm tắt cách sử dụng của kit Plant Total RNA Extraction Miniprep system. sản phẩm có kích thước 669bp:. sản phẩm có kích thước 474bp:. sản phẩm có kích thước 185 bp:. Thực hiện phản ứng Monoplex RT-PCR:. Chuẩn bị phản ứng RT:. RNA của virus CymMV: sử dụng primer CymMV CP-R1.. RNA của virus ORSV: sử dụng primer ORSV CP-R1..

Study on differentially expressed genes related to defoliation traits in two alfalfa varieties based on RNA-Seq

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RNA extraction and RNA-Seq library construction. Total RNA was extracted from three biological replicates of the leaves of each M. Finally, Butterfly analyzed the paths from the de Bruijn graphs that were taken by reads and pairs of reads, and the complete transcripts and unigenes sets were ob- tained from the outputs [54]..

Phytochemical and comparative transcriptome analyses reveal different regulatory mechanisms in the terpenoid biosynthesis pathways between Matricaria recutita L. and Chamaemelum nobile L.

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RNA extraction, library construction, and RNA sequencing Total RNA was extracted separately from flowers of German chamomile and Roman chamomile using the modified CTAB (cetyl trimethyl ammonium bromide) method with three biological replicates [52]. The German chamomile and Roman chamomile unigenes were then aligned to each other by the RBH method described in Tai et al.

Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq

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To determine whether Chrom-EX PE technology is applicable to large and non-histone protein or chromatin complexes, we performed ChIP-seq for RNA polymerase II (RNAP II) in two pairs of FFPE and frozen mouse liver tissues. As expected, RNA Pol II peaks shown in the IGV browser overlap with H3K4me3 marks in TSSs of actively transcribed genes (Fig. These results indicate that Chrom-EX PE is applicable to at least some non-histone protein or chromatin complex in archived FFPE tissues..

RNA isolation from cell free – Saliva of water buffalo

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High quality RNA isolation from ployphenol-, polysaccharide-and protein-rich tissues of lentil (Lens culinaris). 3 Biotech, 3(2), pp.109-114.. and Fu, F., 2013.. Biosensors and Bioelectronics, 45, pp.108-113.. Single- step method of RNA isolation by acid guanidinium thiocyanate-phenol- chloroform extraction. Analytical biochemistry, 162(1), pp.156-159 Li, F., Kaczor-Urbanowicz, K. Clinical chemistry, 64(7), pp.1085-1095.. Plant Molecular Biology Reporter, 15(3), pp.263-272.

Extraction techniques in analytical science

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To be aware of the important variables in performing solid phase extraction.. To be aware of the potential of solid phase extraction for on-line operation.. To be aware of the practical applications of solid phase extraction.. It is the nature of the functional groups that determines the classification of the sorbent. Figure 3.4 The five stages of operation of solid phase extraction. conditioning of the sorbent;. loading of the aqueous sample;. elution of the compound of interest..