RNA-sequencing has become one of the most used high-throughput approaches to gain knowledge about the expression of all different RNA subpopulations. However, technical artifacts, either introduced during library preparation and/or data analysis, can influence the detected RNA expression lev...
Normalization of RNA-sequencing (RNA-seq) data has proven essential to ensure accurate inference of expression levels. Here, we show that usual normalization approaches mostly account for sequencing depth and fail to correct for library preparation and other more complex unwanted technical effects. We...
Library preparation and RNA sequencing. RNA samples were sent to Beijing Novogene Bioinformatics ® ™ ®Technology Co., Ltd., where the libraries were produced and sequenced. Briefly, the RNA-seq libraries were gen- erated using the NEBNext Ultra RNA Library Prep Kit for ...
At the library preparation stage, sequence-dependent variation in amplification generates heterogeneous coverage artifacts [4,5] that lead to differ- ences in exon read counts even in constitutively spliced genes. At the sequencing stage, cluster generation allows sequencing of...
The pair end sequencing libraries for RNA-seq were prepared using illumina TruSeq® RNA Library Preparation Kit as per manufacturer's protocol (illumina®, San Diego, CA). Library quality control and quantification were performed on Caliper LabChip GX using HT DNA High Sensitivity Assay Kit. ...
RNA extraction, library preparation and RNASeq To obtain time course transcriptomes for each of the behavioral castes, we extracted total RNA to prepare sequencing libraries for Illumina short-read sequenc- ing. Two frozen steel ball bearings (5/32″ type 2B, grade 300, Wheels Manufacturing) ...
Kit v2 (Life Technologies). These samples were sequenced in a total of four runs, three in the Ion Torrent using an Ion 318 chip and the fourth in the Ion Proton with the PI chip. Library construction and sequencing were performed by OMICS Solutions (Santiago, Chile). The same RNA-Seq ...
Our algorithm exploits disambiguation information provided by the distribution of insert sizes generated during sequencing library preparation, and takes advantage of base quality scores, strand and read pairing information if available. Empirical experiments on synthetic datasets show that the algorithm ...
RNA isolation, cDNA library preparation and sequencing. Total RNA was isolated using the TRIzol method from six biological replicates of leaf and root tissues. About 500 mg tissue was ground into a fine powder using liquid nitrogen, and the powdered tissue was transferred to DEPC-treated ...
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. NRS–122–2002) with 500 ng of total RNA. Accurate quantitation of cDNA libraries was performed using the QuantiFluor dsDNA System (Promega). The size range of the final cDNA libraries ...