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Multiple definitions of the term "batch effect" have been proposed in the literature. Lazar et al. (2013) noted, "Providing a complete and unambiguous definition of the so-called batch effect is a challenging task, especially because its origins and the way it manifests in the data are not completely known or not recorded."
Design is a fundamental step of a particular RNA-Seq experiment. Some important questions like sequencing depth/coverage or how many biological or technical replicates must be carefully considered. Design review. [5] PROPER: PROspective Power Evaluation for RNAseq.
Most high-throughput, next generation sequencing platforms produce shorter read lengths compared to Sanger sequencing.These new platforms are able to generate large quantities of data in short periods of time, but until methods were developed for de novo assembly of large genomes from short read sequences, Sanger sequencing remained the standard method of creating a reference genome. [10]
The sequencing platform to be used is chosen depending on different factors such as laboratory's research objectives, personal experience and skill levels. So far, the Illumina MiSeq system has proven to be the most commonly used platform for infectious disease research, pathogen surveillance, and pathogen discovery in research and public ...
Whereas high sequence coverage for a genome may indicate the presence of repetitive sequences (and thus be masked), for a transcriptome, they may indicate abundance. In addition, unlike genome sequencing, transcriptome sequencing can be strand-specific, due to the possibility of both sense and antisense transcripts. Finally, it can be difficult ...
[1] [2] [3] Perturb-seq combines multiplexed CRISPR mediated gene inactivations with single cell RNA sequencing to assess comprehensive gene expression phenotypes for each perturbation. Inferring a gene’s function by applying genetic perturbations to knock down or knock out a gene and studying the resulting phenotype is known as reverse ...
The small fragments (historically 27 nucleotides long, but now limited only by sequencing technologies) from the very beginnings of mRNAs (5' ends of capped transcripts) are extracted, reverse-transcribed to cDNA, PCR amplified (if needed) and sequenced. CAGE was first published by Hayashizaki, Carninci and co-workers in 2003. [1]
Cross-linking and immunoprecipitation (CLIP, or CLIP-seq) is a method used in molecular biology that combines UV crosslinking with immunoprecipitation in order to identify RNA binding sites of proteins on a transcriptome-wide scale, thereby increasing our understanding of post-transcriptional regulatory networks.