In this week’s Genome Biology, Niall Lennon and his Broad Institute colleagues present a scalable, fully automated process for the construction of sequence-ready barcoded libraries for use with 454 technology. Lennon and his colleagues devised a method that minimizes sample-handling errors and cross-contamination by using the end-to-end barcoding of plasticware and the molecular DNA barcoding of constructs. The team also describes their automation-friendly clean-up steps utilizing magnetic bead-based size selection, which further eliminate potential sources of error. The team writes that using their methodology, a technician can create 96 sequence-ready 454 libraries in just two days.
Researchers at the Walter and Eliza Hall Institute of Medical Research in Parkville, Australia, present an application for performing Gene Ontology analysis on RNA-seq data, which they’ve dubbed GOseq. GOseq attempts to combat the issues of standard RNA-seq data analysis methods, including biased results from the over-detection of differential expression for long and highly expressed transcripts. Additionally, the team demonstrates that the application of their GOseq methodology to a prostate cancer data set shows that GOseq highlights results more consistent with the known biology than existing methods do.
In another advance online publication in Genome Biology this week, Kankshita Swaminathan of the University of Illinois at Urbana-Champaign and her colleagues suggest that a version of the sorghum genome may be a useful reference in the assembly of a gene-space sequence for Miscanthus x giganteus (Mxg), a perennial grass. Swaminathan’s team surveyed the Mxg genome using 454 pyroseqeuncing of genomic DNA and Illumina sequencing-by-synthesis of small RNA. In doing so, they found that the coding fraction of the Mxg genome has a high level of sequence identity relative to that of other grasses. Their examination also showed that most of the 24-nucleotide small RNAS found are derived from these repetitive sequences; the team confirmed the hypothesized origins of Mxg and suggests that the sorghum genome might be useful as a reference sequence for other Andropogoneae grasses, which have recently emerged as candidate crops for bioenergy.
Indiana University School of Medicine researchers, along with a collaborator at Washington University, suggest candidate genes for alcohol preference in reciprocal congenic rats. The team compared gene expression in five brain regions of alcohol-naïve inbred alcohol-preferring and alcohol non-preferring congenic rats. The team found that more cis-regulated candidate genes for alcohol consumption that lie within the chromosome 4 quantitative trait locus were differentially expressed between the two types of rats. Fewer trans-regulated probesets were detected, the team wrote, and most differed in only one brain region. To confirm their findings, the team performed quantitative real-time PCR; they selected 10 genes to analyze, based on previous literature reporting about their possible involvement in pathways related to alcohol-seeking behavior, and, among them, 79 percent were differentially expressed in the same direction.