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Here, we describe in details a whole microarray transcriptome dataset produced from tsetse flies symbionts, Sodalis glossinidius and Wigglesworthia glossinidia.
Sequences obtained by qPhage plus pyrosequencing were similar to a dataset produced from conventional Sanger-sequenced transducing-units (TU), with no biases due to GC content, codon usage, and amino acid or peptide frequency.
The method has been tested on a simulated dataset produced from mixtures of DNA extracted from four 1000 Genomes Project sample and four spatially separated samples from a primary, untreated high-grade ovarian tumor.
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Applying GET to transcriptomic datasets produced from tissue development studies the results correlated well with developmental stages.
In datasets produced from the ddRADseq protocol, a third bias is associated with the length of restriction fragments.
Despite the negative correlations, this location was included in the mixed datasets produced from the site-specific model selection.
Our genome browser, Trackster, is motivated by the need to enable visual exploration of increasingly large datasets produced from high-throughput sequencing data.
The sparse datasets produced from the ddRADseq protocol introduce a high sampling error to allelic ratio calls, increasing the uncertainty of SNP calls and an increased incidence of coordinates that appear as a SNP in one dataset but not another.
Furthermore, the analysis of Neiman et al. [ 17] is based on a mixture of datasets produced from different sampling approaches and methods ranging from mtDNA sequencing to tissue grafts.
Table 2 lists gene fusions found and summarizes results obtained from the variant analysis pipelines for each tumor; input to this pipeline was the gene expression and variant datasets produced from the tumor transcriptome pipeline.
In this study, by re-analyzing some of the transcriptomic datasets produced from normal human tissues in the Gene Expression Omnibus (GEO), we identified a set of 56 genes whose transcript profiles are endowed with strong tissue-specific properties for 24 different tissue types under the disease-free condition.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com