De Coster Wouter, De Rijk Peter, De Roeck Arne, De Pooter Tim, D’Hert Svenn, Strazisar Mojca, Kristel Sleegers and Van Broeckhoven Christine
Researchers from VIB Center for Molecular Neurology, Antwerp Belgium and University of Antwerp assess using the ONT Promethion for Structural Varian detection in the genome of Yoruban reference individual NA19240. Several variant calling tools were evaluated and compared to short-read sequencing variant calls. A scalable workflow is discussed and future study is considered.
The BluePippin was used for High Pass DNA size selection prior to library construction.
Effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the differentiation of embryonic stem cells towards pancreatic lineage and pancreatic beta cell function
John A. Kubi, Andy C.H. Chen, Sze Wan Fong, Keng Po Lai, Chris K.C. Wong,
William S.B. Yeung, Kai Fai Lee, Yin Lau Lee
From the University of Hong Kong and Hong Kong Baptist University, this study examines the effect of low exposure of a dioxin (TCDD) on embryonic stem cells. Previous animal studies had linked high dioxin exposure to susceptibility to type 2 diabetes. Results indicated altered methylation patterns in stem cell genes associated with insulin secretion. The authors suggest that early embryonic exposure to TCDD may affect pancreatogenesis.
The BluePippin was used to size select libraries prior to bisulfite conversion and reduced representation bisulfite sequencing.
Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures
Benoît Castandet, Arnaud Germain, Amber M. Hotto, and David B. Stern
Researchers present a protocol called Terminome-Seq that they developed to catalog RNA transcript termini in chloroplast DNA of Arabidopsis thaliana. RNA-seq libraries are prepared for the simultaneous analysis of primary and processed 5’ ends, and 3’ends. The authors indicate that the method helps define promoter sequences, regulatory untranslated regions, and the potential for sense-antisense pairing.
Pippin Prep was used to remove products below 200 bp.
Boyce Thompson Institute, Ithica NY
Cornell University, Ithaca,
Université Paris-Saclay, France
Tricia L. Rubi, L. Lacey Knowles, Ben Dantzer
In this preprint, researchers developed method the study epigenetic markers on historically preserved deer mouse specimens using ddRAD-seq and bisulfite sequencing. The oldest group of specimens was 76 years old.
The Pippin Prep was used to size select ddRAD libraries prepared with an extra bisulfite conversion step. Size selection: 376-412 bp and 325-425 bp for higher and lower concentration preps, respectively.
University of Michigan
Comparison of RNA isolation and library preparation methods for small RNA sequencing of canine biofluids
Candice P. Chu, Mary B. Nabity
From the Department of Veterinary Pathobiology at Texas A&M, this study evaluates best practices for small RNA sequencing from canine biofluid samples (serum and urine). The study compares RNA-seq results after using three commercial RNA extraction kits for each biofluid type, and two sequencing library construction kits. A recommendation is provided for isolation/construction for each biofluid, with supporting data.
The PippinHT was used to isolate the small RNA libraries prior to sequencing.
Veterinary Clinical Pathology