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Author Archives: Alex
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
April 2019 Authors: Benoît Castandet, Arnaud Germain, Amber M. Hotto, and David B. Stern Info: 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 … more »
Posted in Citation
Tagged new method, Pippin Prep, terminome-seq
Comments Off on 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
Museum epigenomics: characterizing cytosine methylation in historic museum specimens
April 2019 Authors: Tricia L. Rubi, L. Lacey Knowles, Ben Dantzer Info: 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 … more »
Posted in Citation
Tagged ddRADseq, Pippin Prep
Comments Off on Museum epigenomics: characterizing cytosine methylation in historic museum specimens
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 … more »
Sequencing of human genomes with nanopore technology
April 2019 Authors: 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, … more »
Posted in Citation
Tagged BluePippin, ONT, oxford nanopore, wgs
Comments Off on Sequencing of human genomes with nanopore technology
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 … more »
Posted in Citation
Tagged new method, Pippin Prep, TIPseq, transposon
Comments Off on Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome
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 … more »
AGBT 2019 Re-Cap
AGBT 2019 was a smashing success this year. Featuring a triumphant return to Marco Island FL with postcard perfect weather, the science was (as usual) top-notch. The renovated Marriott greatly upgraded its conference facilities and added an attractive new tower … more »
Posted in Blog
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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 … more »
Posted in Citation
Tagged BluePippin, iso-seq, isoseq
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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 … more »
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 … more »
Posted in Citation
Tagged CpG island, MED-seq, methylation, PippinHT
Comments Off on Gestational jet lag predisposes to later-life skeletal and cardiac disease