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- The haplotype-resolved T2T carnation (Dianthus caryophyllus) genome reveal the correlation between genome architecture and gene expression
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- The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation
- Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method
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Tag Archives: PippinHT
Identification of a precursor processing protease from the spider Cupiennius saleiessential for venom neurotoxin maturation
February 2018 Authors: Nicolas Langenegger, Dominique Koua, Stefan Schürch, Manfred Heller, Wolfgang Nentwig and Lucia Kuhn-Nentwig Info: In this paper, scientists from the University of Bern and collaborators report the identification and purification of a protease that’s an important neurotoxin … more »
A Look Back at 2017
As we start to make lists of New Year’s resolutions (with bets on how long they’ll last), it’s the perfect time for a moment to absorb the themes and highlights of 2017. In our corner of the world, that means … more »
Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
December 2017 Authors: Ruben Boers, Joachim Boers, Bas de Hoon, Christel Kockx, et al. Info: Scientists at Erasmus Medical Center determined that analysis of genome-wide methylation is challenging when fragment sizes are too small and that better epigenetic results are … more »
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
November 2017 Authors: Mircea Cretu Stancu, Markus van Roosmalen, Ivo Renkens, Marleen Nieboer, et al. Info: Scientists used the Oxford MinION nanopore sequencer with a novel pipeline, NanoSV, to detect structural variants from the genomes of two patients. They found … more »
Posted in Citation
Tagged oxford nanopore, PippinHT
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Circulating Tumor DNA Easier to Spot with Size Selection
A bioRxiv preprint from scientists at Cancer Research UK and Cambridge University Hospitals offers a look at how DNA size selection can be used to enhance results of circulating tumor DNA studies. Their analysis indicates that adding a simple sizing … more »
Posted in Blog
Tagged cell-free DNA, ctDNA, PippinHT
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Micro RNA’s (miRNA’s) may help explain expression of multiple genes in Alzheimer’s Frontal Cortex
September 2017 Authors: James Bennett and Paula Keeney Info: Scientists from Neurodegeneration Therapeutics used RNA-seq to compare microRNAs found in Alzheimer’s brain samples and controls. They identified 55 up-regulated genes and 191 down-regulated genes in the Alzheimer’s samples. PippinHT was … more »
A SINE insertion in ATP1B2 in Belgian Shepherd dogs affected by spongy degeneration with cerebellar ataxia (SDCA2)
August 2017 Authors: Nico Mauri, Miriam Kleiter, Elisabeth Dietschi, Michael Leschnik, et al. Info: Scientists in Europe and the US studied the genetic basis for a neurodegenerative disorder in dogs. Through whole genome sequencing data, they found a SINE insertion … more »
For 10x Genomics Workflow, Broad Institute Uses PippinHT Size Selection
At the Broad Institute, scientist Michelle Cipicchio is part of the technology development team responsible for optimizing new methods or sample types before they’re implemented on the organization’s industrial-scale exome and whole-genome sequencing pipeline. Recently, she’s been working with the … more »
Posted in Blog
Tagged 10x Genomics, PippinHT
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PacBio Users: Size Selection Is Essential for Generating Excellent Results
The Sage Science team was delighted to attend and co-sponsor PacBio’s annual East Coast user group meeting in Baltimore last week, particularly since there was a half-day session devoted to our favorite subject: sample prep. There were plenty of customer … more »
Preprint Highlights Utility of Size Selection for Nanopore Studies
A recently shared preprint demonstrates the effectiveness of size-selection for nanopore sequencing, relying on the PippinHT automated DNA sizing platform for high-throughput pipelines. “Mapping And Phasing Of Structural Variation In Patient Genomes Using Nanopore Sequencing” comes from lead author Mircea … more »
Posted in Blog
Tagged oxford nanopore, PippinHT
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