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Recent Posts
- New BluePippin 2.5% Agarose Cassettes Provide High Size Selection Accuracy Between 100-600bp
- Enriching for Answers in Rare Diseases
- Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
- New PippinHT Cassette: >10kB High-Pass with Internal Standards
- Genome-wide comparative analysis of variability and population structure between autochthonous Turkish chicken breeds and commercial hybrid lines
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Author Archives: Alex
Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying blaNDM-1 on a Multidrug Resistance Plasmid
July/August 2016 Authors: Sean Conlan, Anna F. Lau, NISC Comparative Sequencing Program, Tara N. Palmore, Karen M. Frank, and Julia A. Segre Info: NIH scientists sequenced the genome of the first blaNDM-1-positive strain of Klebsiella pneumoniae detected in the institute’s hospital. They found three plasmids, … more »
Posted in Citation
Tagged BluePippin, PacBio
Comments Off on Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying blaNDM-1 on a Multidrug Resistance Plasmid
Circulating Extracellular RNA Markers of Liver Regeneration
July 2016 Authors: Irene K. Yan, Xue Wang, Yan W. Asmann, Hiroaki Haga, Tushar Patel Info: Mayo Clinic researchers performed partial hepatectomies in mice and then monitored RNA activity in serum samples to find a signature associated with liver regeneration. … more »
Posted in Citation
Tagged cfRNA, Illumina, MiSeq, Pippin Prep, RNA sequencing
Comments Off on Circulating Extracellular RNA Markers of Liver Regeneration
Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads
July 2016 Authors: Jiaqiang Dong, Yaping Feng, Dibyendu Kumar, Wei Zhang, Tingting Zhu, Ming-Cheng Luo, and Joachim Messing Info: Scientists from Rutgers University and the University of California, Davis, analyzed copy number variation in the highly repetitive maize genome using … more »
Posted in Citation
Tagged BluePippin, High Pass, PacBio
Comments Off on Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads
Genome-wide identification of enhancer elements
June 2016 Authors: Sarah Tulin, Julius C. Barsi, Carlo Bocconcelli, and Joel Smith Info: The authors (from Woods Hole and Cal Tech) present a genome-wide regulatory element database for the sea urchin embryo. To do this, they developed a new … more »
PI3K/AKT Signaling Regulates H3K4 Methylation in Breast Cancer
June 2016 Authors: Jennifer M. Spangle, Koen M. Dreijerink, Anna C. Groner, Hailing Cheng, Carolynn E. Ohlson, Jaime Reyes, Charles Y. Lin, James Bradner, Jean J. Zhao, Thomas M. Roberts, and Myles Brown Info: In this breast cancer research study, … more »
Posted in Citation
Tagged ChIP-Seq, Illumina, Pippin Prep
Comments Off on PI3K/AKT Signaling Regulates H3K4 Methylation in Breast Cancer
Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing
June 2016 Authors: Shruthi Sridhar Vembar, Matthew Seetin, Christine Lambert, Maria Nattestad, Michael C. Schatz, Primo Baybayan, Artur Scherf, and Melissa Laird Smith Info: Scientists in France and the US used PacBio sequencing to characterize the AT-rich genome of this … more »
Posted in Citation
Tagged BluePippin, High Pass, Pippin Pulse
Comments Off on Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing
A survey of the sorghum transcriptome using single-molecule long reads
June 2016 Authors: Salah E. Abdel-Ghany, Michael Hamilton, Jennifer L. Jacobi, Peter Ngam, Nicholas Devitt, Faye Schilkey, Asa Ben-Hur & Anireddy S. N. Reddy Info: In this publication, scientists from Colorado State University and the National Center for Genome Resources … more »
Posted in Citation
Tagged BluePippin, isoseq, PacBio, RNAseq, transcriptome
Comments Off on A survey of the sorghum transcriptome using single-molecule long reads
PELE-seq Increases SNP Calling Accuracy by Reducing Sequencing Errors
Scientists at the University of Oregon have published a new method to detect PCR and sequencing errors that should help other researchers track rare SNPs with greater accuracy. PELE-seq, which gets our vote for best new protocol name, can be … more »
Posted in Blog
Tagged ddRADseq, genotyping, HiSeq, Illumina, Methods, Pippin Prep
Comments Off on PELE-seq Increases SNP Calling Accuracy by Reducing Sequencing Errors
High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
June 2016 Authors: Jessica L. Preston, Ariel E. Royall, Melissa A. Randel, Kristin L. Sikkink, Patrick C. Phillips, and Eric A. Johnson Info: Scientists at the University of Oregon developed a new protocol to reduce sequencing and PCR errors, resulting … more »
Posted in Citation
Comments Off on High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)
Low-Coverage Sequencing No Challenge for Structural Variant Detection
Is it really possible to detect somatic structural variants accurately from a single sequencing read? A new protocol from scientists at the Albert Einstein College of Medicine in New York and Voronezh State University in Russia was designed to do … more »
Posted in Blog
Tagged Ion Torrent, PippinHT
Comments Off on Low-Coverage Sequencing No Challenge for Structural Variant Detection