Micro RNA’s (miRNA’s) may help explain expression of multiple genes in Alzheimer’s Frontal Cortex
September 2017
Authors:
James Bennett and Paula Keeney
Info:
Scientists from Neurodegeneration Therapeutics used RNA-seq to compare microRNAs found in Alzheimer’s brain samples and controls. They identified 55 up-regulated genes and 191 down-regulated genes in the Alzheimer’s samples. PippinHT was used for small RNA size selection ahead of sequencing on an Illumina NextSeq500.
Citation:
Journal of Systems and Integrative Neuroscience
http://www.oatext.com/micro-rnas-mirnas-may-help-explain-expression-of-multiple-genes-in-alzheimers-frontal-cortex.php#Article
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