RNA-seq library construction
RNaseIII and T4 Polynucleotide Kinase sequence biases and solutions during RNA-seq library construction
... recognizes RNA secondary structure and digests the middle of double stranded RNA ...of RNA-seq found that RNaseIII caused pile- up mapping of RNA-seq data because of its ...
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An automated method for efficient, accurate and reproducible construction of RNA seq libraries
... the construction of next-generation RNA-seq libraries, especially for trancriptome-based annotation of larger ...high-throughput RNA-seq library construction, ...
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A High-Throughput Method for Illumina RNA-Seq Library Preparation.
... for construction of RNA-sequencing (RNA-Seq) libraries are expensive and/or difficult to scale for high-throughput ...total RNA as a starting point. We provide a cost-effective ...
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A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters
... the library preparation ...high-throughput RNA sequencing strategy that has significantly lowered the library prepar- ation cost ...small RNA library preparation. We note that both the ...
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CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification
... Library Construction and Sequencing Illumina’s directional RNA sequencing protocol was used with the following ...of RNA was used as ...amplified RNA repre- sents only mRNA sequences ...
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The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia
... of library preparation on mRNA expression estimates, we prepared i) total, ii) PA, and iii) RD processed RNA isolates from two leukemia patient samples and four breast cancer cell lines and measured the ...
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Assessment of transcript reconstruction methods for RNA-seq
... from RNA-seq data should be interpreted with care, and those critical to an experimental study should be subjected to independ- ent ...novel RNA discovery can improve with increased read depth, but ...
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Re-using public RNA-Seq data
... This work aims to give an overview of main processes of RNA-Seq data analysis. It de- scribes a selection of tools to conduct expression analysis and describes their algorithms. Thesis also gives an ...
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Studying bacterial transcriptomes using RNA-seq
... directions RNA-seq datasets have proved to be highly consistent, when comparing either technical or biological replicates, making them appropriate for expression studies [ 10,50 ...the RNA before ...
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Assessment of transcript reconstruction methods for RNA-seq
... from RNA-seq data should be interpreted with care, and those critical to an experimental study should be subjected to independ- ent ...novel RNA discovery can improve with increased read depth, but ...
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Normalization of RNA-Seq
... EDASeq implements four within-lane normalization methods, namely: loess robust local regression of read counts (log) on a gene feature such as GC-content ( loess ), global-scaling betwee[r] ...
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SCRABBLE: single cell RNA seq imputation constrained by bulk RNA seq data
... Discussion SCRABBLE addresses several deficiencies of existing methods. First, several methods impute dropout events by using cell-cell distance, as quantified by either Euclidean distance or kernel distance. Such ...
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RNA-seq analysis in R
... Rank the genes by statisical significance - you will need to create a new ranking value using -log10({p value}) * sign({Fold Change}).. Run fgsea using the new ranked genes and the H pat[r] ...
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Construction of competing endogenous RNA networks from paired RNA-seq data sets by pointwise mutual information
... We propose a novel method for constructing ceRNA networks from paired RNA-seq data sets. This method identifies the over expressed lncRNAs from the lncRNA expression data of the normal and tumor samples. ...
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VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
... in the pipeline, permitting construction of a pipeline most appropriate for the data under examination. Snakemake was built with the concept of parallelization in mind enabling VIPER to make use of its ability to ...
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Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers
... or RNA, have become increasingly common [ 46 ], and they are more severely affected by PCR ...starting RNA, causing low library ...single-cell, RNA-seq and small RNA-seq ...
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RNA-seq: impact of RNA degradation on transcript quantification
... variable RNA quality (PCs 4 and 5; Additional file 4: Figure S2 and Additional file 3: Table ...quality RNA cluster by individual, data from RNA samples that experienced high yet similar degradation ...
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RNA Preparation, QC and Shipping for RNA-Seq Applications
... A Sample Submission Form (provided by e-mail at time of order), a copy of the quote or purchase order, as well as any relevant QC and safety data must accompany each package to be shipped, for each service project. For ...
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Gel-seq: A Method for Simultaneous Sequencing Library Preparation of DNA and RNA Using Hydrogel Matrices
... labeled RNA/cDNA were processed with the Gel-seq protocol, while lanes labeled RNA show a separation of just gDNA and ...and RNA/cDNA ...
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Bioinformatics for RNA‐Seq Data Analysis
... successful library preparation with kits designed for degraded ...the RNA samples have been addressed, one must then choose whether to profile the total RNA space or the mRNA space ...most ...
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