Author Archives: Alex

Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing

Posted on July 24, 2017 by Alex

July 2017 Authors: Fabio Zanini, Johanna Brodin, Jan Albert, Richard Neher Info: Researchers in Germany and Sweden expounded on a previous deep sequencing study of HIV-1 populations to evaluate challenges such as error profiles and proper controls. For the whole … more »

Posted in Citation | Tagged | Comments Off on Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing

For 10x Genomics Workflow, Broad Institute Uses PippinHT Size Selection

Posted on July 18, 2017 by Alex

At the Broad Institute, scientist Michelle Cipicchio is part of the technology development team responsible for optimizing new methods or sample types before they’re implemented on the organization’s industrial-scale exome and whole-genome sequencing pipeline. Recently, she’s been working with the … more »

Posted in Blog | Tagged , | Comments Off on For 10x Genomics Workflow, Broad Institute Uses PippinHT Size Selection

PacBio Users: Size Selection Is Essential for Generating Excellent Results

Posted on July 6, 2017 by Alex

The Sage Science team was delighted to attend and co-sponsor PacBio’s annual East Coast user group meeting in Baltimore last week, particularly since there was a half-day session devoted to our favorite subject: sample prep. There were plenty of customer … more »

Posted in Blog | Tagged , , , , | Comments Off on PacBio Users: Size Selection Is Essential for Generating Excellent Results

Preprint Highlights Utility of Size Selection for Nanopore Studies

Posted on June 29, 2017 by Alex

A recently shared preprint demonstrates the effectiveness of size-selection for nanopore sequencing, relying on the PippinHT automated DNA sizing platform for high-throughput pipelines. “Mapping And Phasing Of Structural Variation In Patient Genomes Using Nanopore Sequencing” comes from lead author Mircea … more »

Posted in Blog | Tagged , | Comments Off on Preprint Highlights Utility of Size Selection for Nanopore Studies

The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly

Posted on June 25, 2017 by Alex

June 2017 Authors: An-Yun Chang, Stephane Castel, Evan Ernst, Hyun Soo Kim, Robert Martienssen Info: Cold Spring Harbor Laboratory researchers studied the Rct1 protein in S. pombe and found that it is involved in processing pericentromeric transcripts into siRNAs. For … more »

Posted in Citation | Tagged , , | Comments Off on The Conserved RNA Binding Cyclophilin, Rct1, Regulates Small RNA Biogenesis and Splicing Independent of Heterochromatin Assembly

Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports the expression of active dense gene clusters

Posted on June 25, 2017 by Alex

June 2017 Authors: Kobe Yuen, Brian Slaughter, and Jennifer Gerton Info: Scientists in Kansas used the 4C-seq method to study the chromosome complex condensin II in mouse and human genomes. They found that it plays a role in maintaining high … more »

Posted in Citation | Tagged | Comments Off on Condensin II is anchored by TFIIIC and H3K4me3 in the mammalian genome and supports the expression of active dense gene clusters

Creighton Lab Boosts Yield, Sequencing Efficiency with BluePippin

Posted on June 13, 2017 by Alex

At Creighton University in Omaha, Neb., Dr. Anna Selmecki’s lab explores various fungal species to understand genome instability, pathogenesis, and the acquisition of drug resistance. For these investigations, her team relies heavily on whole genome sequencing, using both the Illumina … more »

Posted in Blog | Tagged , , , | Comments Off on Creighton Lab Boosts Yield, Sequencing Efficiency with BluePippin

Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1

Posted on June 12, 2017 by Alex

June 2017 Authors: Dóra Tombácz, Zsolt Csabai, Attila Szűcs, Zsolt Balázs, et al. Info: Scientists from Hungary and California conducted isoform sequencing with PacBio to analyze the transcriptome of herpes simplex virus type 1. They discovered dozens of previously unidentified … more »

Posted in Citation | Tagged , , | Comments Off on Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1

Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

Posted on June 10, 2017 by Alex

June 2017 Authors: Jason Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, Kin Fai Au Info: In this F1000 publication, scientists describe an evaluation of long-read sequencing technologies, finding that PacBio provides better data … more »

Posted in Citation | Tagged , , | Comments Off on Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

Posted on May 25, 2017 by Alex

May 2017 Authors: Franchini P, Monné Parera D, Kautt AF, Meyer A Info: Scientists from the University of Konstanz modified the original ddRAD-seq protocol to make it faster, more cost-effective, and higher-capacity. They report results from validating the new method … more »

Posted in Citation | Tagged , , | Comments Off on quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage