Further development of 5′ specific RNA-seq protocols
5′RNA Seq identifies Fhl1 as a genetic modifier in cardiomyopathy
... 1367 specific induction of iFhl1, a novel transcript that uses an alterna- tive start-site and incorporates 16 additional amino ...acids. Further studies will be needed to determine whether altered protein ...
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FlyAtlas 2: a new version of the Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
... of RNA The tissue/Qiazol samples were thawed and vortexed for 30 s to ensure that the tissues were ...one further chlo- roform ...the RNA pu- rified using a Qiagen miRNeasy mini kit according to the ...
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Dynamics of gene silencing during X inactivation using allele specific RNA seq
... (ElDorado 12–2010) selecting RefSeq genes (NCBI m37 genome assembly; MM9; Additional file 3: Table S2). Calling of allele-specific gene expression Within the individual samples, we used the mapped tags to ...
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Haplotype and isoform specific expression estimation using multi mapping RNA seq reads
... simultaneously, MMSEQ can be used to detect opposing imbalances between isoforms of the same gene directly. Discussion We have presented a pipeline and statistical method that can disaggregate expression between isoforms ...
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Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
... platform. Further- more, the computational requirements of modeling indivi- dual reads increasing proportionately with read depth, which, in the case of RSEM, is exacerbated further by the use of ...
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Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
... platform. Further- more, the computational requirements of modeling indivi- dual reads increasing proportionately with read depth, which, in the case of RSEM, is exacerbated further by the use of ...
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Recommendations for accurate resolution of gene and isoform allele-specific expression in RNA-seq data
... Discordant direction of ASE SNP imbalance explained by splicing patterns While there are several examples of genes with SNPs showing strong concordant direction of imbalance in these data, multiple examples exist of ...
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VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
... a specific reference genome. In RNA-seq, the reads after alignment are quantified on a per gene or per transcript basis to discern information regarding the level of gene expression in a population ...
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Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers
... or RNA, have become increasingly common [ 46 ], and they are more severely affected by PCR ...three specific challenges for PCR duplicate ...starting RNA, causing low library ...of protocols ...
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Identification of differentially expressed genes in the development of osteosarcoma using RNA-seq
... In conclusion, we identified 111 DEGs and 235 DEGs between primary OS and normal controls and between metastatic OS and primary OS, respectively. The potential functions of dysregulated genes in primary OS and metastasis ...
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RNA-Seq Analyses Identify Frequent Allele Specific Expression and No Evidence of Genomic Imprinting in Specific Embryonic Tissues of Chicken
... question. RNA-Seq is emerging as an excellent tool for this purpose, as it surveys the global gene expression and therefore is able to examine the phenomenon of genomic imprinting at the genome-wide ...
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Bioinformatics for RNA‐Seq Data Analysis
... expressed genes. Finally, pathway or network level analyses are performed to gain biological insight through systems biology approaches. 4.1. Quality check and preprocessing of raw reads Poor‐quality read data can arise ...
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Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states
... allele-specific RNA- seq of early (extra-)embryonic tissues and various types of pluripotent cell lines in vitro using an isogenic mouse F1 genotype, allowing genome-wide comparative analy- sis of ...
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Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models
... genes further raised questions about the relevance of using the elav-driven down-regulation of Smn to characterize neuronal specific gene expression ...neuronal specific-expression of the anti-Smn ...
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Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq
... Single-cell RNA-seq has been established as a reliable and accessible technique enabling new types of analyses, such as identifying cell types and studying spatial and temporal gene expression variation and ...
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Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri
... Table S3, Fig. 5). The most thoroughly investigated genes with regard to cellular differentiation are glsA, hsp70A, lag, and regA [8, 27, 30, 32, 33, 35–42, 45, 46, 49, 58–64, 73] (Fig. 2). Both glsA and hsp70A ...
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Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data.
... We first consider a model-based simulator. This is useful as evidence that all the methods have been implemented properly. To be realistic, the parameters are based on real data and per- formed as follows: first, the ...
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Exon-intron chain reconstruction of circular RNA using RNA-Seq
... circular RNA expressing genes were enriched for development, signalling and neural ...during development before the CNS was ...or specific regulation and suggested, that although this increase ...
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RNA-Seq Analysis in Fruit Science: A Review
... principle, RNA-Seq allows analysis of all expressed transcripts, with three key goals: (i) annotating the structures of all transcribed genes including their 5′ and 3′ ends and all splice junctions ...
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Synthetic spike-in standards for RNA-seq experiments
... external RNA standards are a pow- erful tool for routine assessment of RNA-seq experiments and during experimental and computational protocol ...of RNA-seq quantification, tested the ...
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