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Nucleic Acids Research Papers on FIN-Seq, ChlamDB, BBCancer

Researchers from Harvard and the Broad Institute describe a sequencing strategy for assessing specific cell types in flash frozen central nervous system samples from brain tissue banks. The method — known as "frozen immunolabeled nuclei sequencing," or FIN-Seq — includes steps for isolating cell type specific-nuclei with antibody labeling and fluorescence-activated cell sorting, followed by RNA sequencing, the team says, making it possible to profile transcriptomes in a given CNS cell type in an affordable manner. "With FIN-Seq, we isolated and profiled specific excitatory and inhibitory neuronal subtypes from frozen human cerebral cortex tissue, some of which had been stored for over 15 years," the authors report. "We also extended the method to a different part of the CNS by isolating and profiling cone photoreceptors from the frozen human retina."

A Lausanne University Hospital and University of Lausanne team introduces version 2.0 of a database called ChlamDB, designed for comparing genome sequences in bacteria from the Chlamydiae phylum and related bacterial species. "As a central resource for researchers working on chlamydia, chlamydia-related bacteria, verrucomicrobia, and planctomyces, ChlamDB facilitates the access to comprehensive annotations, integrates multiple tools for comparative genomic analyses and is freely available," the researchers write, noting that the database currently contains 277 genomes and includes tools for retrieving, annotating, analyzing, and comparing the genomes and specific features in them.

Finally, Chinese researchers report on an open access online database for tallying and analyzing array- or RNA sequencing-based expression profiles for half a dozen RNA types in samples from individuals with or without cancer. The BBCancer resources contains information on messenger RNA, long non-coding RNA, microRNA, circular RNA, transfer RNA-derived fragment, and/or Piwi-interacting RNA patterns in nearly 7,200 samples spanning 15 cancer types — a set that encompasses more than 5,000 blood-based samples, including RNA types in extracellular vesicles and circulating tumor cells. "[W]e believe that BBCancer will be of significant benefit to the community and boost further advances in developing blood-based biomarkers for the early detection of cancer," they write.