RNA-seq Analysis
RNA-seq Analysis of Solanesol Biosynthesis Genes in Nicotiana tabacum
... for RNA-seq ...perform RNA-seq and quantitative real-time PCR (qRT-PCR) analyses, the leaf tissues were harvested from four growing stages of tobacco plants, ...
18
RNA-Seq Analysis in Fruit Science: A Review
... used RNA-Seq to perform global transcriptome profiling on Moneymaker tomato fruits at the turning ripening ...deficiency. RNA-Seq analysis were performed using the Illumina Genome ...
7
DegNorm: normalization of generalized transcript degradation improves accuracy in RNA seq analysis
... RNA-seq is currently the most prevailing method for profiling transcriptional activities using high-throughput sequencing technology [1]. The sequencing tag count per unit of transcript length is used to ...
18
Fast and accurate single cell RNA seq analysis by clustering of transcript compatibility counts
... single-cell RNA-seq analysis inter- active for the first time: sensitivity of results to parameters and annotations can be easily explored and analyses can be easily reproduced by individuals without ...
14
RNA-SEQ Analysis of Localized MST1/STK4 Expression in Prostate Cancer
... RNA-Seq technology is capable of producing millions of sequencing reads in a single experiment.The depth to which a sample can be sequenced typically exceeds the experimental demands.Determining the ...
102
RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection
... methylation analysis, miRNA expres- sion profiling, and also in non-model organisms as the de novo transcriptome sequencing ...transcriptome analysis can be performed faster and more easily, because it does ...
16
Accuracy, robustness and scalability of dimensionality reduction methods for single cell RNA seq analysis
... (8 data sets), 10X Genomics (6 data sets), Smart-Seq (5 data sets), inDrop (1 data set), RamDA-seq (1 data set), sci-RNA-seq3 (1 data set), SMARTer (5 data sets), and others (3 data sets). In ...
21
RNA-seq analysis of synovial fibroblasts brings new insights into rheumatoid arthritis
... Genes expressed only in control SFs or only in RASFs The top 10 up- and down-regulated genes expressed only in control SFs or only in RASFs are presented in Table 3. An expanded list of the top 50 genes expressed only in ...
16
RNA-Seq analysis reveals new evidence for inflammation- related changes in aged kidney
... Total RNA was isolated from the cortex of kidney sample using the miRNeasy Mini Kit (Qiagen, Hilden, ...An RNA sequencing library was generated using TruSeq RNA sample preparation Kit according to ...
12
RNA-seq analysis of Lgr6(+) stem cells and identification of an Lgr6 isoform
... on RNA-seq of Lgr6 + versus Lgr6 - cells from hair follicles and IFE of haired ...more RNA and our read counts were at least 100x higher allowing more reliable quantification of low abundant ...
33
Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists
... Both pipelines agree on most DE genes called (Fig. 5a) but each identifies a small number of unique DE genes (Fig. 5b). The numbers of up- or down-regulated DE genes detected by Granatum are closer, whereas in ASAP a lot ...
12
Improving the RNA-Seq analysis pipeline: read alignment and expression level quantification
... Another resulting trend is the one that relates the tools accuracy to the algorithm and data structure employed. Among the four best performing tools, CLC and STAR use an uncompressed suffix array, Novoalign exploits a ...
210
Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts
... Single-cell RNA-Seq (scRNA-Seq) has proved to be a powerful tool for probing cell states [1–5], defining cell types [6–9], and describing cell lineages ...bulk RNA-Seq have been ...
28
LncRNA SNHG8 is identified as a key regulator of acute myocardial infarction by RNA-seq analysis
... analyzing RNA-seq data and established a global triple network via the Gene Expression Omnibus (GEO) repository to explore the potential molecular mechanisms of ...
17
The bench scientist's guide to statistical analysis of RNA Seq data
... of RNA-Seq analysis A first potential limitation of this approach is that it may be too conservative, as evidenced by the 2,242 marginally significant genes that were removed from the final optimized ...
10
An iteration normalization and test method for differential expression analysis of RNA-seq data
... Current RNA-seq analysis methods typically standardize data between samples by scal- ing the number of reads in a given library to a common value across all sequenced libraries in the ...LONGSAGE- ...
10
A survey of best practices for RNA seq data analysis
... and analysis scenarios in which RNA-seq can be ...ferent analysis strategies depending on the organism be- ing studied and their research ...mapping RNA-seq reads onto the ...
19
Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes
... standard RNA-Seq analysis pathways when dealing with viruses and, with guidance, become aware of the biological characteristics and genome structure of the virus being ...
9
Methods, challenges and potentials of single cell RNA seq
... To fully exploit this potential, several requirements must be met. Precise parameter estimation for mathematical models of transcriptional regulation is usually based on single-molecule fluorescent in situ hybridization ...
11
Methods For Robust Quantification Of Rna Alternative Splicing In Heterogeneous Rna-Seq Datasets
... as RNA-binding protein (RBP) and micro RNA (miRNA) binding sites, whether due to sequence alone or a change in the mRNA’s secondary structure that affects binding of the ...
98