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PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences
... Random sequences are generated to determine the likelihood of a high score occurring by ...random sequences when searching a database of a particular ...large sequences of length m and n, the evalue ... See full document
108
Detection of Murine Leukemia Virus in the Epstein-Barr Virus-Positive Human B-Cell Line JY, Using a Computational RNA-Seq-Based Exogenous Agent Detection Pipeline, PARSES
... harbor exogenous agents such as the human tumor vi- ruses Epstein-Barr virus (EBV) and human ...throughput sequencing should provide unparalleled insights into the microbiomes of tissue culture cell ...our ... See full document
389
Deep Sequencing of Foot-and-Mouth Disease Virus Reveals RNA Sequences Involved in Genome Packaging
... Next-generation sequencing. RNA was extracted from samples of clarified infected cell lysate or purified virus using TRIzol and prepared for next-generation sequencing as described previously ...and ... See full document
24
RNA CoMPASS: RNA Comprehensive Multi-Processor Analysis System for Sequencing
... in RNA CoMPASS, and we show the limitations of the existing tools and provide our novel solution to solve these ...of RNA CoMPASS. In this chapter, we describe two frameworks used in RNA CoMPASS, ... See full document
7
Exploring the unmapped DNA and RNA reads in a songbird genome.
... the RNA sequencing ...generation sequencing methods have not been fully utilized in the host-parasite studies of great tits, which might prove to be a successful avenue to explore in addition to ... See full document
129
A novel noncoding FKRP mutation in early onset limb-girdle muscular dystrophy
... The Leu276Ile variant is the most common FKRP patho- genic variant. 1 The second variant found in our patient, c.- 253+4A>G, has not been reported previously. Because this variant destroys the canonical splice donor ... See full document
22
Identification and characterization of microRNAs
... number of novel sequences identified by miRNA-Sequencing. B) Pie chart depicts the total number of mature miRNA sequences 156.. identified by miRNA-Sequencing analysi[r] ... See full document
6
A comprehensive review of web-based resources of non-coding RNAs for plant science research
... sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information. The lncRNAdb can be searched by keywords, including ... See full document
37
Unprecedented High Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing
... RNA sequencing. RNA was prepared by using an RNeasy kit (Qiagen, ...stationary-phase RNA were treated with Terminator 5=-phosphate-dependent exonuclease (Epicenter, USA) to enrich 5=- ... See full document
87
The E2A splice variant E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical development
... Cis-regulatory sequences associated with E2A occupancy in embryonic NSCs were identified by comparison of enriched binding sites with randomly selected genomic DNA ...cis-regulatory sequences associated ... See full document
14
Genetics Analysis of the Biggest Cashew Tree in the World
... The sequencing reaction utilized the Big Dye® Terminator ...Cycle Sequencing Kit reagent (Applied Biosystems) and by precipitation reaction Ethanol/EDTA/sodium ...The analysis was made from automated ... See full document
81
Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker
... The reads from the FASTQ files were mapped against the GRCh37.75 human reference genome by using STAR (https://github.com/alexdobin/STAR/releases) version 2.4.0. The output files in BAM format were analyzed by RSEM ... See full document
71
Design and computational analysis of single cell RNA sequencing experiments
... single-cell sequencing technologies and con- comitant advances in computational and statistical ...single-cell RNA-seq, as well as other types of single-cell ... See full document
129
Statistical Methods for Gene Differential Expression Analysis of RNA-Sequencing
... GO analysis on recently published RNA-Seq data that examined the effect of dexamethasone treatment on primary neural progenitor cells of embryonic mice (Frahm et ...enrichment analysis to each ... See full document
70
Integrated TCGA analysis implicates lncRNA CTB-193M12.5 as a prognostic factor in lung adenocarcinoma
... In this study, we took advantage of large-scale expres- sion profiles and a systems biology strategy to identify lncRNAs that were significantly regulated in lung cancer specimens, and were strongly co-expressed with a ... See full document
16
Adaptive Immunity Restricts Replication of Novel Murine Astroviruses
... Pfam analysis (17) and showing significant similarity (minimal e-value cutoff of 1e ⫺5 ) to those of known astroviruses by BLASTp ...FSFinder analysis (46) confirmed that the downstream sequence may form a ... See full document
134
Detection of vesicular stomatitis virus RNA and its defective-interfering particles in individual mouse brains.
... For differentiation of hybridizable sequences found in the RNA of DI particles from complementary or identical sequences in the L mRNA or standard genomic RNA of VSV, RNA obtained from m[r] ... See full document
108
<p>Bioinformatics Analysis and RNA-Sequencing of SCAMP3 Expression and Correlated Gene Regulation in Hepatocellular Carcinoma</p>
... We initially evaluated SCAMP3 transcription levels in multiple cancers from TCGA. Data from the Oncomine database showed that mRNA expression was signi fi - cantly higher in breast cancer, leukemia and especially in Liver ... See full document
7
SNP detection using RNA-sequences of candidate genes associated with puberty in cattle.
... using sequences from Brangus heifers, the VEP tool was used to predict the effect of the variation on the protein as per the intra-gene locus of the 1157 SNPs (Figure ... See full document
8
High-resolution ISR amplicon sequencing reveals personalized oral microbiome
... Background: Sequencing of the 16S rRNA gene has been the standard for studying the composition of microbial ...level analysis using whole metagenome shotgun sequencing has significant limitations ... See full document
8
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