Citations

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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A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans

February 2020

Authors:
Yuehui Zhao, Lijiang Long, Jason Wan, Shweta Biliya, Shannon C. Brady, Daehan Lee, Akinade Ojemakinde, Erik C. Andersen, Fredrik O. Vannberg, Hang Lu, Patrick T. McGrath

Info:
Researchers studying genetic adaptive changes using C. elegans recombinant inbred lines (RIL). A single RIL with a high fitness and exploration phenotype was observed that did not share these traits relative to the parental strains. Short-read sequencing indicated a spontaneous complex rearrangement of the rcan-1 gene. This rearrangement was resolved into five unique tandem inversion/duplications using Oxford Nanopore long-read sequencing. The authors suggest that colonization of new environments can create evolutionary pressure to produce complex rearrangements that can act to modify gene expression in ways besides increased gene dosage.

BluePippin was used to size select 10-50kb DNA fragments for Oxford Nanopore MinION library preparation.

Author Affiliations:
Georgia Institute of Technology, Atlanta, Georgia
Northwestern University, Evanston, Illinois

Citation:
PLOS Genetics
DOI: 10.1371/journal.pgen.1008606

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Amplification-free long read sequencing reveals unforeseen CRISPR-Cas9 off-target activity

February 2020

Authors:
Ida Höijer, Josefin Johansson, Sanna Gudmundsson, Chen-Shan Chin, Ignas Bunikis, Susana Häggqvist, Anastasia Emmanouilidou, Maria Wilbe, Marcel den Hoed, Marie-Louise Bondeson, Lars Feuk, Ulf Gyllensten, Adam Ameur

Info:
In this preprint, the authors propose a method for screening for off off-target CRISPR/Cas9 sites using PacBio and Oxford Nanopore sequencing. The amplification-free method purifies and sequences both on-target and off-target cut sites from a DNA sample. The method could prove useful for improving gRNA design and screening and suggests the ability to develop de Novo guides as opposed to requiring a reference genome. SageELF was used to fractionate (1-18KB) SMRTBells for PacBio Hi-Fi circular consensus sequencing.

Author Affiliations:
Uppsala University, Sweden
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
Boston Children’s Hospital, Boston, MA
Monash University, Melbourne, Australia
Citation:
bioRxiv
DOI: 10.1101/2020.02.09.940486

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Capture of complete ciliate chromosomes in single sequencing reads reveals widespread chromosome isoforms

December 2019

Authors:

Kelsi A. Lindblad, Jananan S. Pathmanathan, Sandrine Moreira, John R. Bracht, Robert P. Sebra, Elizabeth R. Hutton & Laura F. Landweber

Info:
Researchers sequenced the whole genome of Oxytricha trifallax, a model protozoan ciliate, using long read sequencing. Since Oxytricha trifallax has 16,000 chromosomes that only average 3.2 kpb in length, its much of the genome was sequenced with chromosomal-length single reads without assembly. By comparing the results to the reference sequence assemblies the researchers demonstrated that short read sequencing can mask considerable structural variation.
BluePippin was used to size-select PacBio SMRT libraries.

Author Affiliations:
Columbia University, New York, NY
Princeton University, Princeton, NJ
American University, Washington DC
Icahn School o f Medicine at Mt Sinai, New York, NY
Cold Spring Harbor Laboratories, Cold Spring Harbor, NY

Citation:
BMC Genomics
DOI: 10.1186/s12864-019-6189-9

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Comparison of mitochondrial DNA variants detection using short- and long-read sequencing

August 2019

Authors:
Ahmed N. Alkanaq, Kohei Hamanaka, Futoshi Sekiguchi, Masataka Taguri, Atsushi Takata, Noriko Miyake, Satoko Miyatake, Takeshi Mizuguchi, Naomichi Matsumot

Info:
The genotypes of mitochondrial DNA variants are compared using both short-read (Illumina Hi-SeqX10) and long-read (PacBio Sequel) sequencing. DNA samples from three individuals with mitochondrial disease used for the study. The authors conclude that although long reads have higher error rates (though random) and short-read have higher accuracy (but with systemic errors), PacBio sequencing can overcome is error bias with 37 reads.

BluePippin was used to select >10kb SMRTbell libraries using the High-Pass protocol.

Author Affiliations:
Yokohama City University

Citation:
Journal of Human Genetics
DOI: 10.1038/s10038-019-0654-9

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