Citations

Comparison of RNA isolation and library preparation methods for small RNA sequencing of canine biofluids

Authors:
Candice P. Chu, Mary B. Nabity

Info:
From the Department of Veterinary Pathobiology at Texas A&M, this study evaluates best practices for small RNA sequencing from canine biofluid samples (serum and urine). The study compares RNA-seq results after using three commercial RNA extraction kits for each biofluid type, and two sequencing library construction kits. A recommendation is provided for isolation/construction for each biofluid, with supporting data.

The PippinHT was used to isolate the small RNA libraries prior to sequencing.

Citation:
Veterinary Clinical Pathology
DOI: 10.1111/vcp.12743

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Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome

March 2019

Authors:
Jared P. Steranka, Zuojian Tang, Mark Grivainis, Cheng Ran Lisa Huang, Lindsay M. Payer, Fernanda O. R. Rego, Thiago Luiz Araujo Miller, Pedro A. F. Galante, Sitharam Ramaswami, Adriana Heguy, David Fenyö, Jef D. Boeke & Kathleen H. Burns

Info:
A new technique is described; Transposon Insertion Profiling (TIPseq). The method uses vectorette PCR and paired-end Illumina sequencing to map (LINE-1, L1) retrotransposon insertions in the human genome. A detailed protocol is provided.

Pippin Prep is used to remove fragments below 400 bp from libraries prior to sequencing.

Author Affiliations:
Johns Hopkins University School of Medicine, Baltimore, MD
NYU Langone Health, New York, NY,
Hospital Sírio-Libanês, São Paulo, Brazil
Universidade de São Paul, São Paulo, Brazil

Citation:
Mobile DNA
DOI: 10.1186/s13100-019-0148-5

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Identification of whole blood mRNA and microRNA biomarkers of tissue damage and immune function resulting from amphetamine exposure or heat stroke in adult male rats

February 2019

Authors:
Luısa Camacho, Camila S. Silva, Joseph P. Hanig, Robert P. Schleimer, Nysia I. George, John F. Bowyer

Info:
A report from the USDA and others evaluate the effect of amphetamine and methamphetamine toxicity on immune systems and tissues using rat models. In particular, hyperthermic effects, due to the drug exposure or environmentally induces were studied. With hyperthermia, an increase in organ related transcripts were indicated and as was possible liver damage. In addition, changes to the immune system suggest modified risk of for HIV and other infections.

The PippinHT was used to isolated small RNA (15-35bp) Illumina libraries prior to sequencing.

Citation:
PLOS One
DOI: 10.1371/journal.pone.0210273

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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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