Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures
Benoît Castandet, Arnaud Germain, Amber M. Hotto, and David B. Stern
Researchers present a protocol called Terminome-Seq that they developed to catalog RNA transcript termini in chloroplast DNA of Arabidopsis thaliana. RNA-seq libraries are prepared for the simultaneous analysis of primary and processed 5’ ends, and 3’ends. The authors indicate that the method helps define promoter sequences, regulatory untranslated regions, and the potential for sense-antisense pairing.
Pippin Prep was used to remove products below 200 bp.
Boyce Thompson Institute, Ithica NY
Cornell University, Ithaca,
Université Paris-Saclay, France
Tricia L. Rubi, L. Lacey Knowles, Ben Dantzer
In this preprint, researchers developed method the study epigenetic markers on historically preserved deer mouse specimens using ddRAD-seq and bisulfite sequencing. The oldest group of specimens was 76 years old.
The Pippin Prep was used to size select ddRAD libraries prepared with an extra bisulfite conversion step. Size selection: 376-412 bp and 325-425 bp for higher and lower concentration preps, respectively.
University of Michigan
Comparison of RNA isolation and library preparation methods for small RNA sequencing of canine biofluids
Candice P. Chu, Mary B. Nabity
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.
Veterinary Clinical Pathology
Rory Bowden, Robert W. Davies, Andreas Heger, Alistair T. Pagnamenta, Mariateresa de Cesare, Laura E. Oikkonen, Duncan Parkes, Colin Freema, Fatima Dhalla, Smita Y. Patel, Niko Popitsch, Camilla L.C. Ip, Hannah E. Roberts, Silvia Salatino, Helen Lockstone, Gerton Lunter, Jenny C. Taylor, David Buck, Michael A. Simpson, Peter Donnelly
The potential of using Oxford Nanopore Technologies MinION sequencer is evaluated for Whole Genome Sequencing (WGS). A reference sample (NA112878) was sequenced alongside an individual with clinical indications. The authors applied novel bioinformatic approaches to the analysis and identify innovations that could significantly improve the platform’s potential for clinical WGS.
BluePippin was used to enrich DNA fragments >6kb using the High-Pass protocol prior to library construction.
Wellcome Centre for Human Genetics, Oxford UK
Hospital for Sick Children, Toronto CA
Oxford University, Oxford UK
National Institute for Health Research, Oxford UK
Children’s Cancer Research Institute, Vienna Austria
Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome
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
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.
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