In a paper published online in advance in Nucleic Acids Research this week, investigators at Uppsala University in Sweden describe a scalable protocol for targeted re-sequencing of candidate genes using a non-PCR-based version of the selector method. Using an RCA-based multiple displacement amplification rather than PCR, the team says researchers can generate an amplification that is "easily integrated with shotgun library construction for short-read sequencing platforms." In testing their method, the Uppsala team achieved 94 percent specificity and 98 percent coverage in enriching for and sequencing 501 exons from 38 cancer-associated genes. The procedure, which "readily [enables] detection of copy-number variations," the team writes, "can be carried out in [less than] 24 hours and does not require any dedicated instrumentation."
Researchers at Korea's Ewha Womans University describe an updated version of miRGator, "an integrated system for functional investigation of microRNAs" online in Nucleic Acids Research this week. miRGator v2.0, the team writes, contains information about more than 8,000 "human miRNA expression profiles under various experimental conditions" and "paired expression profiles of both mRNAs and miRNAs," more than 300 "gene expression profiles under miRNA-perturbation (e.g. miRNA knockout and overexpression), known/predicted miRNA targets, and miRNA-disease associations." The most recent version of the system allows researchers to readily access complex associations "using an interactive network visualization interface," the authors report.
The International Nucleotide Sequence Database Collaboration this week describes the structure and content of its sequence read archive, a "public repository for the next-generation sequence data." The INSDC team also suggests data submission protocols and "briefly outlines [its] response to the challenge of data growth."
Also in Nucleic Acids Research this week, researchers at Isis Pharmaceuticals report an "approach to deplete snoRNA, small Cajal body RNA, and small nuclear RNA in human and mouse cells by conventional transfection of chemically modified antisense oligonucleotides that promote RNaseH-mediated cleavage of target RNAs." Using their method, the Isis team says that "at least five snoRNAs [can] be depleted simultaneously" in mice by the systematic administration of ASOs.