Citations

Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development

March 2019

Authors:
Andrea Minio, Mélanie Massonnet, Rosa Figueroa-Balderas, Amanda M. Vondras, Barbara Blanco-Ulate, and Dario Cantu

Info:
Researchers used PacBio’s Iso-Seq method to sequence full-length cDNA transcripts from ripening Cabernet Savignon berries resulting in 1,5000 cultivar-specific genes. The authors discuss using transcriptome profiles for comprehensive referencing as an alternative to costly genome referencing.

The BluePippn was used to size select 1-2 kbp, 2-3 kbp, 3-6 kbp, and 5-10 kbp fractions for cDNA SMRTbell library construction for the Iso-Seq method.

Author Affiliations:
University of California, Davis

Citation:
G3: Genes, Genomes, Genetics
DOI: 10.1534/g3.118.201008

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Enhanced detection of circulating tumor DNA by fragment size analysis

November 2018

Authors:
Florent Mouliere et al.

Info:
This study from Cancer Research UK and a large team of collaborators is a continuation of work evaluating circulating tumor DNA (ctDNA) and the significance of sub-167 base pair cell-free DNA as a marker for tumors. Samples from a cohort of 200 patients were tested and show significantly improved detection of ctDNA by size selecting DNA between 90-150 bp, and using the TAm-Seq technique to detect mutations. PippinHT was used for DNA size selection.

Citation:
Science Translational Medicine
DOI: 10.1126/scitranslmed.aat4921

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Small-seq for single-cell small-RNA sequencing

September 2018

Authors:
Michael Hagemann-Jensen, Ilgar Abdullayev, Rickard Sandberg and Omid R Faridani

Info:
A new protocol from researchers at the Karolinska Institutet and the Ludwig Institute for Cancer Research outline a method for making small RNA sequencing libraries from a single mammalian cell. The method increases sensitivity compared with other methods by using a oligonucleotides to mask ribosomal RNA rather than using a pulldown strategy. Pippin Prep is recommended to isolated miRNA away from other small RNAs.

Citation:
Nature Protocols 13, pages2407–2424 (2018)
10.1038/s41596-018-0049-y

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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 monitoring the disease in real time to prevent future epidemics. Pippin Prep used to size select RNA-seq libraries for paired end Illumina sequencing.

Citation:
Science 361 (6405), 894-899
doi: 10.1126/science.aat7115

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Highly sensitive detection of mutations in CHO cell recombinant DNA using multi‐parallel single molecule real‐time DNA sequencing

June 2018

Authors:
Joseph Cartwright, Karin Anderson, Joseph Longworth, Philip Lobb, and David James

Info:
To improve the quantitative assessment of recombinant DNA in cell lines, University of Sheffield scientists and collaborators developed a PacBio-based method for high-throughput rDNA sequence analysis. The protocol can sequence 40,000 individual recombinant DNA molecules at once to find point mutations. BluePippin was used for purification prior to sequencing.

Citation:
Biotechnology and Bioengineering
doi: 10.1002/bit.26561

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