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
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
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
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
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