Citations

A long-read RNA-seq approach to identify novel transcripts of very large genes

July 2020

Authors:
Prech Uapinyoying, Jeremy Goecks, Susan M. Knoblach, Karuna Panchapakesan, Carsten G. Bonnemann, Terence A. Partridge, Jyoti K. Jaiswal, and Eric P. Hoffman

Info:
Scientists researching muscular disorders present a method for studying gene expression of large RNA transcripts. The PacBio Iso-Seq method allows the sequencing of large transcripts for the identification of isoforms and alternative splicing. However, it has not been amenable to accurate quantitation of expression. Here the scientists combine Iso-Seq with PacBio’s HiFi high consensus accuracy method to show differential gene expression of large transcripts in muscles as well as identify and quantitate previously unannotated ones.

BluePippin was used to size select 5-10kb cDNA fragments for PacBio Iso-Seq library construction, and a second size selection step to remove unligated adapters.

Author Affiliations:
Center for Genetic Medicine Research, Children’s Research Institute, Washington D.C.

Department of Genomics and Precision Medicine, The George Washington University School of Medicine and Health Sciences, Washington, D.C.
National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD

Computational Biology Program, Oregon Health and Science University, Portland, OR

Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY

Citation:
Genome Research
DOI: 10.1101/gr.259903.119.

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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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