RNA sequencing and mapping
Allelic mapping bias in RNA sequencing is not a major confounder in eQTL studies
... allelic mapping bias is not a major confounder in gene and exon quantifications based on RNA sequencing data, nor a major source of false positive eQTL ...allelic mapping bias and accounting ...
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Mapping human pluripotent stem cell differentiation pathways using high throughput single cell RNA sequencing
... single-cell RNA-sequencing (scRNA-seq), based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body ...
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scDual Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single cell RNA sequencing
... single-cell RNA-sequencing Gal Avital 1,2 , Roi Avraham 3,6 , Amy Fan 3 , Tamar Hashimshony 2 , Deborah ...single-cell RNA-sequencing method, scDual-Seq, that simultaneously captures both host ...
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RNA CoMPASS: RNA Comprehensive Multi-Processor Analysis System for Sequencing
... High-throughput RNA sequencing has revolutionized the field of transcriptomics allowing researchers to characterize gene expression within an organism under a variety of conditions [Costa et ...New ...
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Discovering cancer-associated transcripts by RNA sequencing
... transcript. We believe many of these are produced from unspliced pre-mRNA molecules and do not represent functional RNA products. Third, we removed transcripts that lacked a completely unambiguous genomic DNA ...
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Concurrent and Accurate RNA Sequencing on Multicore Platforms
... The following two configurations employ 8 threads, fur- ther reducing the total execution time, but with a different distribution: 1+3+1+3 and 1+4+1+2, with the first one obtaining slightly better results (312.33s vs ...
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A telescope for the RNA universe : novel bioinformatic approaches to analyze RNA sequencing data
... or mapping reads to the reference sequence means finding the most probable location (origin) of the reads in the ...substitutions. RNA-Seq reads can be aligned to the reference transcriptome, as well as to ...
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IVT seq reveals extreme bias in RNA sequencing
... total RNA-seq reac- tion, we subjected this IVT RNA to rRNA depletion and then prepared libraries using the Illumina TruSeq protocol (Figure 1C, IVT ...IVT RNA with various amounts of mouse total ...
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Dissecting organ-specific transcriptomes through RNA-sequencing
... mitochondrial mapping, the per- centage of shared transcripts could still effectively expose the genome usage pattern among organs since all organs shared the same mitochondrial genome, being on the same ...
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PARSES: A Pipeline for Analysis of RNA-Sequencing Exogenous Sequences
... generation sequencing technologies ...from RNA-Seq experiments, solving the problem of mapping reads back to the host organism's genome [2] ...interrogate RNA-Sequencing experiments for ...
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Mapping actionable pathways and mutations in brain tumours using targeted RNA next generation sequencing
... analysis of metabolism by measuring relative expression levels of metabolic enzymes [36, 38]. To analyze clinic- ally actionable pathways we expanded the assay with smMIPs to quantify expression levels of and detect mu- ...
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RNA sequencing for the study of splicing
... of RNA molecules present in eukaryote cells, splicing emerges as the most prominent mechanism for mes- sage ...throughput sequencing to RNA, known as RNA sequencing, have opened new ...
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The Stanford RNA Mapping Database for sharing and visualizing RNA structure mapping experiments
... The RNA sequence being studied, its secondary structure, standardized annotations, and free text comments are also ...probed RNA; the second of length 3 that describe the probe used; and the third is a four ...
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Single-cell RNA-sequencing of the brain
... Single‑cell RNA‑sequencing data analysis Two important questions which need to be addressed in scRNA-seq assays are the minimum number of cells to be sequenced and the sequencing depth at which the ...
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Deciphering the RNA landscape by RNAome sequencing
... large RNA classes, among which we could also identify differential expressed RNAs, suggesting functional roles in the cellular cisplatin response (intronic, Supplemental Dataset 2; intergenic, Supplemental Dataset ...
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User guide for mapping by sequencing in Arabidopsis
... of mapping-by- ...scheme. Mapping-by-sequencing with backcross popula- tions requires higher coverage for optimal mapping results as compared to outcross ...for mapping- ...
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Progression of RNA-sequencing to single-cell applications
... Manufacturer's descriptions of their protocols can be understated, presumably not wanting to disappoint customers who would try the protocol at the limit of its ability, at least RNA input amounts are ...
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Statistical Design and Analysis of RNA Sequencing Data
... For both replicated and unreplicated scenarios the proposed balanced block designs benefit from both the NGS platform design and multiplexing. These designs are as good as, if not better than, their unblocked ...
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Annotating genomes with massive scale RNA sequencing
... called RNA-Seq [20-26]. Before the development of the RNA-Seq technology, large- scale RNA analysis could be performed with two types of ...signature sequencing (MPSS) [29], were based on the ...
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Statistical methods for the analysis of RNA sequencing data
... and sequencing technologies combined with statistical data analyses provide researchers with the ability to explore and understand complex biological ...and RNA-seq data, there is a need to evaluate ...
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