- Next generation sequencing (NGS) data analysis, Chi-seq, RNA-seq ...
Evaluation of Unbiased Next Generation Sequencing of RNA (RNA seq) as a Diagnostic Method in Influenza Virus Positive Respiratory Samples
... available data, it is difficult to define abundance thresholds that may indicate a pathogenic infection, even if the clinical context is supportive of such a ...
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Sí, Se Puede (Yes, We Can), Culturally Relevant Biographies: A study on the impact of culturally relevant biographies on social studies instruction
... of next generation sequencing (NGS) technologies and provides better measurement of levels of transcripts and their ...plaguing RNA-Seq experiments is ...entire RNA-Seq ...
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Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes
... major RNA sequencing ...platforms. RNA-Seq of polyadenylated RNAs (A) or total RNA after rRNA depletion (B) enables profiling at a high resolution but requires a well-curated reference ...
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A software tool ‘CroCo’ detects pervasive cross-species contamination in next generation sequencing data
... recent RNA-seq datasets, includ- ing two of our own, as a proof of concept (see details in Methods and Additional file 1: Table ...1). Sequencing experiments differ greatly in their levels of ...
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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
... throughput sequencing should provide unparalleled insights into the microbiomes of tissue culture cell ...our RNA-seq analysis pipeline, PARSES (Pipeline for Analysis of ...
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Whole exome sequencing of a single osteosarcoma case—integrative analysis with whole transcriptome RNA-seq data
... The protocols and informed consent form used in this study were approved by the Ethical Review Committee on Human Research of the University of Tartu. The pa- tient signed a written informed consent, which also in- ...
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Effects of subsampling on characteristics of RNA-seq data from triple-negative breast cancer patients
... optimal sequencing depths with respect to two complementary ...optimal sequencing depth is likely to depend on the bioinformatics ...expression data from DNA microarray experi- ments, such ...
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IVT seq reveals extreme bias in RNA sequencing
... rRNA-depleted data introduced just as much if not ...the RNA-seq data showed nucleotide frequencies characteris- tic of random priming bias (Additional file 8: Figure ...plasmid data ...
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Finding differential splice junctions in RNA-Seq data as transcriptional biomarkers for prostate cancer
... [22]. Next-generation or high-throughput sequenc- ing provides a way to sequence cDNA to study a sample’s mature RNA sequence, which is called RNA sequencing or ...
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Profiling tissue-resident T cell repertoires by RNA sequencing
... available RNA-seq datasets from the TCGA ...[28–30]. Next, we evaluated the differential abundance of CDR3s between tumors and matched normal control tissues for all individuals where the ...
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Software for Estimation of Human Transcriptome Isoform Expression Using RNA-Seq Data
... high-throughput data produced by the next generation sequencing technologies (as described in section ...[23]. Next-generation tools provide excellent genome coverage and base ...
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A survey of best practices for RNA seq data analysis
... of RNA-seq is to esti- mate gene and transcript ...reported RNA-seq gene expression ...the data can find significant differences in gene length between samples that cannot be ...
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Analysis of the Aspergillus nidulans transcriptome using high-throughput RNA sequencing
... to RNA-seq reads, indicating broad transcriptional utilisation of the ...previous sequencing studies. These data also indicate a significant level of antisense transcription, supporting ...
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SCRABBLE: single cell RNA seq imputation constrained by bulk RNA seq data
... Single-cell RNA sequencing (scRNA-seq) has revolution- ized cell biology, enabling studies of heterogeneity and transcriptome dynamics of complex tissues at single-cell ...scRNA-seq ...
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RNA Seq and Bulked Segregant Analysis of Genes Related to High Growth in Ginkgo biloba Half Sibling Families
... mRNA sequencing (RNA-Seq) is a next-generation sequencing technology [12] [13] [14] [15] that has been used widely to authenti- cate and quantify normal and rare transcripts, and ...
22
Genome-Wide Analysis of RNA Secondary Structure in Eukaryotes
... ssRNA- seq) and the tools to infer secondary structure from these data ...reasonable sequencing depth, suggesting that the approach can be scaled up to genome-wide ...input RNA, extent of ...
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Integrated TCGA analysis implicates lncRNA CTB-193M12.5 as a prognostic factor in lung adenocarcinoma
... the RNA sequencing technology has greatly facilitated identifying lncRNAs associated with various ...complex data processing. In contrast, RNA-Seq enjoys a number of advantages, ...
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Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing
... performed next-generation sequencing for both cross-linked and non-cross- linked samples in three biological replicates, subsequently seeing good correlations within each experimental condition ...of ...
15
Transcriptome analysis of endometrial tissues following GnRH agonist treatment in a mouse adenomyosis model
... for analysis during the window of implantation ...high-throughput RNA sequencing (RNA-Seq) data to compare the transcriptomes of endometrial tissues before and after treatment to ...
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The bench scientist's guide to statistical analysis of RNA Seq data
... Soybean plants (Glycine max cv. Be Sweet 292) were grown in environmentally controlled growth cham- bers for six weeks in either ambient or elevated ozone conditions (150 ppb for 8 h d -1 ). Tissue was collected from ...
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