Tag Archives: Pippin Prep

Museum epigenomics: characterizing cytosine methylation in historic museum specimens

April 2019 Authors: Tricia L. Rubi, L. Lacey Knowles, Ben Dantzer Info: 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 … more »

Posted in Citation | Tagged , | Comments Off on Museum epigenomics: characterizing cytosine methylation in historic museum specimens

Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome

March 2019 Authors: Jared P. Steranka, Zuojian Tang, Mark Grivainis, Cheng Ran Lisa Huang, Lindsay M. Payer, Fernanda O. R. Rego, Thiago Luiz Araujo Miller, Pedro A. F. Galante, Sitharam Ramaswami, Adriana Heguy, David Fenyö, Jef D. Boeke & Kathleen … more »

Posted in Citation | Tagged , , , | Comments Off on Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome

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 … more »

Posted in Citation | Tagged , | Comments Off on Genomic and epidemiological monitoring of yellow fever virus transmission potential

Tracking Chikungunya: New Study Traces Outbreak Path

A team of scientists in Brazil, along with collaborators in the U.S. and Europe, used diagnostics and metagenomic sequencing to reconstruct the transmission path of a recent outbreak of chikungunya virus in Maceió. We were honored to donate some lab … more »

Posted in Blog | Tagged , , | Comments Off on Tracking Chikungunya: New Study Traces Outbreak Path

Spread of Chikungunya Virus East/Central/South African Genotype in Northeast Brazil

October 2017 Authors: Antonio Charlys da Costa, Julien Thézé, Shirley Cavalcante Vasconcelos Komninakis, Rodrigo Lopes Sanz-Duro, et al. Info: Scientists in Brazil and collaborators in the U.S. and Europe traced the transmission path of a recent chikungunya virus outbreak. They … more »

Posted in Citation | Tagged , | Comments Off on Spread of Chikungunya Virus East/Central/South African Genotype in Northeast Brazil

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 … more »

Posted in Citation | Tagged | Comments Off on Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes

Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity

July 2017 Authors: Kelley Yan, Olivier Gevaert, Grace Zheng, Benedict Anchang, et al. Info: In this project from scientists at Stanford University School of Medicine and other institutions, comparative RNA-seq was used to analyze putative mouse intestinal stem cells. The … more »

Posted in Citation | Tagged , | Comments Off on Intestinal Enteroendocrine Lineage Cells Possess Homeostatic and Injury-Inducible Stem Cell Activity

Differential regulation of miRNA and mRNA expression in the myocardium of Nrf2 knockout mice

July 2017 Authors: Justin Quiles, Madhusudhanan Narasimhan, Gobinath Shanmugam, Brett Milash, John Hoidal, and Namakkal Rajasekaran Info: Scientists from the University of Alabama at Birmingham and other institutions studied a gene previously associated with oxidative stress, analyzing differential expression in … more »

Posted in Citation | Tagged , , | Comments Off on Differential regulation of miRNA and mRNA expression in the myocardium of Nrf2 knockout mice

ddRAD-seq Study Explores Behavioral Roles in Speciation

A new preprint from the Hoekstra lab at Harvard makes great use of the double digest RAD-seq protocol to better understand reproductive barriers and speciation in closely related species of mice. Since it was the Hoekstra lab that gave us … more »

Posted in Blog | Tagged , | Comments Off on ddRAD-seq Study Explores Behavioral Roles in Speciation

quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

May 2017 Authors: Franchini P, Monné Parera D, Kautt AF, Meyer A Info: Scientists from the University of Konstanz modified the original ddRAD-seq protocol to make it faster, more cost-effective, and higher-capacity. They report results from validating the new method … more »

Posted in Citation | Tagged , , | Comments Off on quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage