Citations

Gestational jet lag predisposes to later-life skeletal and cardiac disease

February 2019

Authors:
Inês Chaves, Bram van der Eerden, Ruben Boers, Joachim Boers, Astrid A. Streng, Yanto Ridwan, Marijke Schreuders-Koedam, Marijn Vermeulen, Ingrid van der Pluijm, Jeroen Essers, Joost Gribnau, Irwin K. M. Reiss & Gijsbertus T. J. van der Horst
Info:
Researchers subjected pregnant mice several protocols that mimic jet lag and evaluated the effect on the subsequent offspring. Along with reduced bone strength and muscle mass, the authors identified hypermethylation of the miR17-92 micro RNA gene cluster and differential methylation within the circadian clock gene.
Methylation was determined using the MeD-seq protocol (Boers et al. 2018). With MeD-seq, PippinHT was used to isolate 32 bp insert sequencing libraries. MeD-seq uses the restriction enzyme LpnPI which cuts at methylation sites but is blocked by fragments smaller than 32 bp.
+Author Affiliations:
University Medical Center Rotterdam, The Netherlands
Citation:
Chronobiology International

DOI: 10.1080/07420528.2019.1579734

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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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Small-seq for single-cell small-RNA sequencing

September 2018

Authors:
Michael Hagemann-Jensen, Ilgar Abdullayev, Rickard Sandberg and Omid R Faridani

Info:
A new protocol from researchers at the Karolinska Institutet and the Ludwig Institute for Cancer Research outline a method for making small RNA sequencing libraries from a single mammalian cell. The method increases sensitivity compared with other methods by using a oligonucleotides to mask ribosomal RNA rather than using a pulldown strategy. Pippin Prep is recommended to isolated miRNA away from other small RNAs.

Citation:
Nature Protocols 13, pages2407–2424 (2018)
10.1038/s41596-018-0049-y

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Genomic and epidemiological monitoring of yellow fever virus transmission potential

August 2018

Authors:
N.R. Faria, et al.

Info:
A large collaboration between international and Brazilian researchers used a suite of epidemiological, spatial, and genomic approaches to characterize Yellow Fever virus transmission in Brazil. The study potentially establishes a framework for monitoring the disease in real time to prevent future epidemics. Pippin Prep used to size select RNA-seq libraries for paired end Illumina sequencing.

Citation:
Science 361 (6405), 894-899
doi: 10.1126/science.aat7115

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Highly sensitive detection of mutations in CHO cell recombinant DNA using multi‐parallel single molecule real‐time DNA sequencing

June 2018

Authors:
Joseph Cartwright, Karin Anderson, Joseph Longworth, Philip Lobb, and David James

Info:
To improve the quantitative assessment of recombinant DNA in cell lines, University of Sheffield scientists and collaborators developed a PacBio-based method for high-throughput rDNA sequence analysis. The protocol can sequence 40,000 individual recombinant DNA molecules at once to find point mutations. BluePippin was used for purification prior to sequencing.

Citation:
Biotechnology and Bioengineering
doi: 10.1002/bit.26561

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