Citations

Fully phased sequence of a diploid human genome determined de novo from the DNA of a single individual

July 2020

Authors:
Ilya Soifer , Nicole L. Fong, Nelda Yi, Andrea T. Ireland, Irene Lam, Matthew Sooknah, Jonathan S. Paw, Paul Peluso, Gregory T. Concepcion, David Rank, Alex R. Hastie, 5 Vladimir Jojic, J. Graham Ruby, David Botstein, Margaret A. Roy
Info:
Researchers at Calico Life Sciences in a collaboration with the platform manufacturers PacBio (sequencing) and BioNano (optical mapping) produced a fully phased de novo assembly of a human genome. 10X Genomics linked-read technology was also used, and a new method is presented that uses Illumina sequencing of flow cytometry-sorted metaphase chmormosomes.
>20KB High-Pass was used on the BluePippin for the construction of SMRTbell library for PacBio RSII sequencing.

Author Affiliations:
Calico Life Sciences LLC, South San Francisco,CA
Pacific Biosciences, Menlo Park, CA
Bionano Genomics, San Diego, CA

Citation:
G3:Genes/Genom/Genetics (Early online)
DOI: 10.1534/g3.119.400995

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Highly accurate long-read HiFi sequencing data for five complex genomes

May 2020
Authors:
Ting Hon, Kristin Mars, Greg Young, Yu-Chih Tsai, Joseph W. Karalius, Jane M. Landolin, Nicholas Maurer, David Kudrna, Michael A. Hardigan, Cynthia C. Steiner, Steven J. Knapp, Doreen Ware, Beth Shapiro, Paul Peluso, David R. Rank

Info:
Pacific Biosciences, in conjunction with their research partners, publicly released (in a BioRxiv preprint) the sequences of five complex genomes that were derived using their high-accuracy circular consensus sequencing (the HiFi method, which resequences 15-20kb SMRTbells up to 30X). The genomes include inbred models Mus musculus (house mouse) and Zea mays,(corn) and complex models Fragaria × ananassa (Strawberries) and Rana muscosa (mountain yellow-legged frog). The fifth sequence was a mock metagenomic bacterial community (ATCC MSA-1003).
Three of the libraries use the SageELF for narrow size selections at ~15KB. The BluePippin was used for one genome (beads were used to size select the metagenomic samples.

Author Affiliations:
Pacific Biosciences, Menlo Park CA
Ravel Biotechnology, San Francisco CA
University of California Santa Cruz, Santa Cruz CA
University of Arizona, Tuscon AR
University of California Davis, Davis CA
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
USDA-ARS, Ithaca NY
Howard Hughes, Medical Institute, University of California Santa Cruz

Citation:
BioRxiv Preprint
DOI: 10.1101/2020.05.04.077180

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Decimated little brown bats show potential for adaptive change

April 2020

Authors:
Giorgia G. Auteri & L. Lacey Knowles

Info:
Little brown bats have experienced a 90% population decline due to fungal pathogen that causes a disease, white-nose syndrome. The authors used ddRADseq to compare surviving and non-surviving individuals. The results indicate shifts in allelic frequencies in genes associated with responses to the disease, suggesting evolutionary adaptation to the syndrome.

Pippin Prep was used to size-select ddRad libraries.

Author Affiliations:
Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI

Citation:
Nature Scientific Reports
DOI: 10.1038/s41598-020-59797-4

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A restriction enzyme reduced representation sequencing approach for low-cost, high-throughput metagenome profiling

April 2020

Authors:
Melanie K. Hess, Suzanne J. Rowe, Tracey C. Van Stijn, Hannah M. Henry, Sharon M. Hickey, Rudiger Brauning, Alan F. McCulloch, Andrew S. Hess, Michelle R. Kirk, Sandeep Kumar, Cesar Pinares-Patiño, Sandra Kittelmann, Graham R. Wood, Peter H. Janssen, John C. McEwan

Info:
The authors present a restriction enzyme reduced representation sequencing (RE-RRS) method for metagenome profiling of livestock rumen microbial communities. The researchers correlate the profiles with methane production from the animals and compare results to previous 16S sequencing benchmarks.

Pippin Prep was used to size-select amplified sequences.

Author Affiliations:
AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
AgResearch Limited, Ruakura Agricultural Centre, Hamilton, New Zealand
AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand

Citation:
PLOS One
DOI: 10.1371/journal.pone.0219882

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Inhalation of lung spheroid cell secretome and exosomes promotes lung repair in pulmonary fibrosis

February 2020

Authors:

Phuong-Uyen C. Dinh, Dipti Paudel, Hayden Brochu, Kristen D. Popowski, M. Cyndell Gracieux, Jhon Cores, Ke Huang, M. Taylor Hensley, Erin Harrell, Adam C. Vandergriff, Arianna K. George, Raina T. Barrio, Shiqi Hu, Tyler A. Allen, Kevin Blackburn, Thomas G. Caranasos, Xinxia Peng, Lauren V. Schnabel, Kenneth B. Adler, Leonard J. Lobo, Michael B. Goshe & Ke Cheng

Info:

Collaborators at North Carolina State University report success treating Idiopathic pulmonary fibrosis (IPF) with inhalation treatment with lung spheroid cell-secretome and exosomes using mouse models. IPF is a fatal and incurable form of interstitial lung disease in which persistent injury results in scar tissue formation.

Pippin Prep was used to isolate microRNA sequencing libraries for studying the microRNA profile of exosomes post-treatment.

Author Affiliations:

North Carolina State University, Raleigh NC

Citation:

Nature Communications
DOI: 10.1038/s41467-020-14344-7

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