Citations

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

June 2019

Authors:
De Coster Wouter, De Rijk Peter, De Roeck Arne, De Pooter Tim, D’Hert Svenn, Strazisar Mojca, Kristel Sleegers and Van Broeckhoven Christine

Info:
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.

Citation:
Genome Research
DOI: 10.1101/gr.244939.118

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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

May 2019

Authors:
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

Info:
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.

Citation:
Environment International
DOI: 10.1016/j.envint.2019.05.079

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Comparison of RNA isolation and library preparation methods for small RNA sequencing of canine biofluids

Authors:
Candice P. Chu, Mary B. Nabity

Info:
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.

Citation:
Veterinary Clinical Pathology
DOI: 10.1111/vcp.12743

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Identification of whole blood mRNA and microRNA biomarkers of tissue damage and immune function resulting from amphetamine exposure or heat stroke in adult male rats

February 2019

Authors:
Luısa Camacho, Camila S. Silva, Joseph P. Hanig, Robert P. Schleimer, Nysia I. George, John F. Bowyer

Info:
A report from the USDA and others evaluate the effect of amphetamine and methamphetamine toxicity on immune systems and tissues using rat models. In particular, hyperthermic effects, due to the drug exposure or environmentally induces were studied. With hyperthermia, an increase in organ related transcripts were indicated and as was possible liver damage. In addition, changes to the immune system suggest modified risk of for HIV and other infections.

The PippinHT was used to isolated small RNA (15-35bp) Illumina libraries prior to sequencing.

Citation:
PLOS One
DOI: 10.1371/journal.pone.0210273

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Enhanced detection of circulating tumor DNA by fragment size analysis

November 2018

Authors:
Florent Mouliere et al.

Info:
This study from Cancer Research UK and a large team of collaborators is a continuation of work evaluating circulating tumor DNA (ctDNA) and the significance of sub-167 base pair cell-free DNA as a marker for tumors. Samples from a cohort of 200 patients were tested and show significantly improved detection of ctDNA by size selecting DNA between 90-150 bp, and using the TAm-Seq technique to detect mutations. PippinHT was used for DNA size selection.

Citation:
Science Translational Medicine
DOI: 10.1126/scitranslmed.aat4921

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