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

Posted in Citation | Tagged , , | Comments Off on Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development

Cancer stem cell–associated miRNAs serve as prognostic biomarkers in colorectal cancer

March 2019

Authors:
Shusuke Toden, Shigeyasu Kunitoshi, Jacob Cardenas, Jinghua Gu, Elizabeth Hutchins, Kendall Van Keuren-Jensen, Hiroyuki Uetake, Yuji Toiyama, and Ajay Goel

Info:
This study evaluates cancer stems cells (CSC) which resist chemotherapy agents and have high tumor initiation capacity. A particular gene variant within these cells, CD44, appears to present a more aggressive phenotype when over expressed. The researchers undertook miRNA profling of the CD44 in a cohort of patients to identify the dysregulated species. They suggest that these miRNAs could be used as prognostic biomarkers or possibly therapeutic targets for patients with colorectal cancer.
For this study, generated several CSC cell lines. ThePippinHT was used to isolate miRNA libraries (148bp).

Author Affiliations:
Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center. Dallas
Baylor Institute for Immunology Research, Dallas
Translational Genomics Research Institute, Phoenix, Arizona
Tokyo Medical and Dental University, Tokyo
Mie University Graduate School of Medicine, Mie, Japan

Citation:
Journal of Clinical Investigation Insight

DOI:10.1172/jci.insight.125294.

Posted in Citation | Tagged , , | Comments Off on Cancer stem cell–associated miRNAs serve as prognostic biomarkers in colorectal cancer

Gestational jet lag predisposes to later-life skeletal and cardiac disease

February 2019

Authors:
Inês Chaves, Bram van der Eerden, Ruben Boers, Joachim Boers, Astrid A. Streng, Yanto Ridwan, Marijke Schreuders-Koedam, Marijn Vermeulen, Ingrid van der Pluijm, Jeroen Essers, Joost Gribnau, Irwin K. M. Reiss & Gijsbertus T. J. van der Horst
Info:
Researchers subjected pregnant mice several protocols that mimic jet lag and evaluated the effect on the subsequent offspring. Along with reduced bone strength and muscle mass, the authors identified hypermethylation of the miR17-92 micro RNA gene cluster and differential methylation within the circadian clock gene.
Methylation was determined using the MeD-seq protocol (Boers et al. 2018). With MeD-seq, PippinHT was used to isolate 32 bp insert sequencing libraries. MeD-seq uses the restriction enzyme LpnPI which cuts at methylation sites but is blocked by fragments smaller than 32 bp.
+Author Affiliations:
University Medical Center Rotterdam, The Netherlands
Citation:
Chronobiology International

DOI: 10.1080/07420528.2019.1579734

Posted in Citation | Tagged , , , | Comments Off on Gestational jet lag predisposes to later-life skeletal and cardiac disease

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

Posted in Citation | Comments Off on Enhanced detection of circulating tumor DNA by fragment size analysis

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

Posted in Citation | Comments Off on Small-seq for single-cell small-RNA sequencing