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RNA preparation methods
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The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter and circularizing the ligation products.
9p
vigalileogalilei
27-02-2022
10
1
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The ability to profile and quantify small non-coding RNAs (sRNAs), specifically microRNAs (miRNAs), using highthroughput sequencing is challenging because of their small size. We developed QsRNA-seq, a method for preparation of sRNA libraries for high-throughput sequencing that overcomes this difficulty by enabling a gelfree separation of fragments shorter than 100 nt that differ only by 20 nt in length.
12p
vigalileogalilei
27-02-2022
14
2
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Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3′ cDNA libraries for dozens of samples, requiring just 2 hours of hands-on time.
15p
vigalileogalilei
27-02-2022
8
2
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A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts in viable single cells, allowing one to disconnect time and place of sampling from subsequent processing steps.
15p
vialfrednobel
29-01-2022
6
0
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This inhibits 3′ adapter ligation and makes library preparation particularly challenging. To reduce bias, the NEBNext kit (New England Biolabs) uses polyethylene glycol (PEG), the NEXTflex V2 kit (BIOO Scientific) uses both randomised adapters and PEG, and the novel SMARTer (Clontech) and CATS (Diagenode) kits avoid ligation altogether. Here we compared these methods with Illumina’s classical TruSeq protocol regarding the detection of normal and 2’ OMe RNAs. In addition, we modified the TruSeq and NEXTflex protocols to identify conditions that improve performance.
16p
vibeauty
23-10-2021
8
0
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Cell type-specific ribosome-pulldown has become an increasingly popular method for analysis of gene expression. It allows for expression analysis from intact tissues and monitoring of protein synthesis in vivo. However, while its utility has been assessed, technical aspects related to sequencing of these samples, often starting with a smaller amount of RNA, have not been reported. In this study, we evaluated the performance of five library prep protocols for ribosome-associated mRNAs when only 250 pg-4 ng of total RNA are used.
16p
vitzuyu2711
29-09-2021
13
1
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3’ RNA sequencing provides an alternative to whole transcript analysis. However, we do not know a priori the relative advantage of each method. Thus, a comprehensive comparison between the whole transcript and the 3′ method is needed to determine their relative merits.
12p
viseulgi2711
31-08-2021
10
1
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RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapter ligation bias with limited evaluation of reverse transcription bias or amplification bias.
21p
visilicon2711
20-08-2021
8
1
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PCR amplification is an important step in the preparation of DNA sequencing libraries prior to high-throughput sequencing. PCR amplification introduces redundant reads in the sequence data and estimating the PCR duplication rate is important to assess the frequency of such reads.
11p
vioklahoma2711
19-11-2020
10
2
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Noises and artifacts may arise in several steps of the next-generation sequencing (NGS) process. Recently, an NGS library preparation method called SMART, or Switching Mechanism At the 5′ end of the RNA Transcript, is introduced to prepare ChIP-seq (chromatin immunoprecipitation and deep sequencing) libraries from small amount of DNA material, using the DNA SMART ChIP-seq Kit.
13p
vicoachella2711
27-10-2020
8
0
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To determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed. Methods: Ten CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system.
14p
vimoscow2711
29-08-2020
4
1
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Two main apple growing provinces (Van and Malatya) of East Anatolia were surveyed for the presence of the Apple mosaic virus (ApMV). Dot-blot hybridization and RT-PCR tests were implemented to investigate the incidence of ApMV, testing a total of 481 samples collected from commercial apple orchards.
8p
vimb123
11-01-2019
20
2
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