mRNA Library Preparation for RNA-seq

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RNA-seq allows for quantiative transcriptomic profiling of biological samples. RNA-seq takes advantage of technological advancements in high-throughput sequencing by converting RNAs of interest to a library of cDNA fragments that can then be sequenced using standard DNA-sequencing technologies. Preparing a sample for RNA-seq typically begins with either rRNA depletion of mRNA enrichment. This is due

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5 Useful R Commands for Working with Big Data

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5 useful R commands for working with big data 1. View a large object (big RData file called object for example) in a manner similar to less in command line. page(object, method=”print”) 2. Listing top n objects in memory. rev(sort(sapply(ls(envir=globalenv()), function(x) { object.size(get(x,env=globalenv())) })))[1:n] 3. Remove all objects except for those contained in a set

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Genome amplification approaches: DOP-PCR, MDA, MALBAC

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DOP-PCR = degenerate oligonucleotide priming polymerase chain reaction Method Overview: In the first cycling stage (5-8 cycles), low-temperature annealing and extension occur at many binding sites in the genome and become tagged with the DOP primer. In the second cycling stage (>25 cycles), annealing temperature is raised, increasing priming specificity during amplification of the tagged

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SNP vs. SNV vs. Mutation

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SNP = single nucleotide polymorphism. As its name suggests, a SNP is a DNA change at the single nucleotide level. By virtue of being a polymorphism, a SNP must occur commonly within a population, with “common” typically being understood as having a minor allele frequency of >1%. The commonality of SNPs generally implies that SNPs

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