Rapid and affordable size-selected PacBio single-molecule real-time sequencing template library construction using the bead-beating DNA extraction method
September 2017
Authors:
Kengo Kato, Masanori Hashino, Tamaki Ito, Mari Matsui, et al.
Info:
Researchers developed and validated a streamlined protocol for PacBio sequencing sample prep. The method involves bead-beating for DNA isolation. For the project, the team used Pippin Pulse to perform automated electrophoresis.
Citation:
J Biol Methods 2017;4(3):e79.
doi: 10.14440/jbm.2017.169
Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes
September 2017
Authors:
Billy Lau and Hanlee Ji
Info:
Scientists aimed to address errors that occur with conventional molecular barcodes for RNA-seq workflows. They developed transposable error-correcting barcodes with tens of billions of unique labels and found that this approach mitigates such problems. They validated the approach in a project that incorporated Pippin Prep to remove PCR products smaller than 500 bp.
Citation:
BMC Genomics 201718:745
doi: 10.1186/s12864-017-4141-4
Complete Genome Sequences of Seven Strains Composing a Model Bacterial Community of Maize Roots
September 2017
Authors:
Ben Niu and Roberto Kolter
Info:
Scientists from Harvard Medical School released the full genome sequences of seven bacterial species they chose for a model community to understand microbial effects on the growth of maize root. They found that these bacteria have protective effects, suppressing the growth of pathogens. Sequencing was performed on the PacBio RS II with BluePippin sizing for 20 Kb libraries.
Citation:
Genome Announc. 2017 Sep; 5(36): e00997-17.
doi: 10.1128/genomeA.00997-17
A SINE insertion in ATP1B2 in Belgian Shepherd dogs affected by spongy degeneration with cerebellar ataxia (SDCA2)
August 2017
Authors:
Nico Mauri, Miriam Kleiter, Elisabeth Dietschi, Michael Leschnik, et al.
Info:
Scientists in Europe and the US studied the genetic basis for a neurodegenerative disorder in dogs. Through whole genome sequencing data, they found a SINE insertion in the ATP1B2 gene that appears to be causative for a subtype of the disorder. The team used PippinHT for size-selecting cDNA fragments prior to sequencing.
Citation:
G3: Genes, Genomes, Genetics
Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles
August 2017
Authors:
Albrecht V, Zweiniger C, Surendranath V, Lang K, et al.
Info:
Scientists in Germany describe a high-throughput approach for characterizing novel HLA alleles. The method involves sequencing the full gene with PacBio and MiSeq. For PacBio sequencing, libraries are sized with BluePippin.
Citation:
HLA. 2017 Aug;90(2):79-87
doi: 10.1111/tan.13057