Tag Archives: BluePippin

Preprint Roundup: Long-Read Sequencing, ddRAD-seq, and a New Look at Viruses

Posted on November 27, 2017 by Alex

We always keep our eyes peeled for interesting new research from scientists using Sage Science automated DNA size selection instruments, and several recent preprints caught our attention. Here’s a look: Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome … more »

Posted in Blog | Tagged , , , | Comments Off on Preprint Roundup: Long-Read Sequencing, ddRAD-seq, and a New Look at Viruses

Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

Posted on November 8, 2017 by Alex

November 2017 Authors: Bing Cheng, Agnelo Furtado, Robert Henry Info: In this study, researchers generated the transcriptome of the tetraploid Arabica coffee bean, focusing on caffeine and sucrose genes for in-depth analysis. They used the PacBio Iso-Seq method with BluePippin … more »

Posted in Citation | Tagged , | Comments Off on Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

Posted on October 31, 2017 by Alex

October 2017 Authors: Maximilian Schmidt, Alxander Vogel, Alisandra Denton, Benjamin Istace, et al. Info: Scientists used Oxford Nanopore technology to sequence Solanum pennellii, a wild species of tomato. They generated a median read length of nearly 12 Kb and produced … more »

Posted in Citation | Tagged , | Comments Off on De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

Assessing a single targeted next generation sequencing for human leukocyte antigen typing protocol for interoperability, as performed by users with variable experience

Posted on October 30, 2017 by Alex

October 2017 Authors: Manish Gandhi, Deborah Ferriola, Curt Lind, Jamie Duke, et al. Info: Scientists from the Mayo Clinic, Children’s Hospital of Philadelphia, and other institutions teamed up to develop a streamlined, NGS-based HLA typing protocol. This method uses the … more »

Posted in Citation | Tagged , , | Comments Off on Assessing a single targeted next generation sequencing for human leukocyte antigen typing protocol for interoperability, as performed by users with variable experience

Comprehensive Transcriptome Profiling of Balding and Non-Balding Scalps in Trichorhinophalangeal Syndrome Type I Patient

Posted on October 30, 2017 by Alex

October 2017 Authors: Yun-Ji Kim, Byulee Yoon, Kyudong Han, Byung Cheol Park Info: Scientists in Korea compared transcriptomes of RNA extracted from balding and non-balding scalp regions on the same patient to understand the genetics of hair loss. They found … more »

Posted in Citation | Tagged , , | Comments Off on Comprehensive Transcriptome Profiling of Balding and Non-Balding Scalps in Trichorhinophalangeal Syndrome Type I Patient

What’s the difference between the 4-10 Kb vs2 and 6-10 Kb vs3 high pass protocols?

Posted on September 15, 2017 by Alex

Customers may have noticed two very similar cassette definitions; 0.75%DF Marker S1 high-pass 4-10kb vs2 and 0.75%DF Marker S1 High-Pass 6-10kb vs3. Since these two protocols cover a similar range, they might seem a bit redundant. However, both of these … more »

Posted in Blog, Tips | Tagged , , | Comments Off on What’s the difference between the 4-10 Kb vs2 and 6-10 Kb vs3 high pass protocols?

Complete Genome Sequences of Seven Strains Composing a Model Bacterial Community of Maize Roots

Posted on September 8, 2017 by Alex

September 2017 Authors: Ben Niu and Roberto Kolter Info: Scientists from Harvard Medical School released the full genome sequences of seven bacterial species they chose for a model community to understand microbial effects on the growth of maize root. They … more »

Posted in Citation | Tagged , | Comments Off on Complete Genome Sequences of Seven Strains Composing a Model Bacterial Community of Maize Roots

Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles

Posted on July 25, 2017 by Alex

August 2017 Authors: Albrecht V, Zweiniger C, Surendranath V, Lang K, et al. Info: Scientists in Germany describe a high-throughput approach for characterizing novel HLA alleles. The method involves sequencing the full gene with PacBio and MiSeq. For PacBio sequencing, … more »

Posted in Citation | Tagged , , , | Comments Off on Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles

Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis

Posted on July 24, 2017 by Alex

July 2017 Authors: Qingshan Xu, Junyan Zhu, Shiqi Zhao, Yan Hou, et al. Info: Scientists from Anhui Agricultural University in China performed long-read transcriptome sequencing of the tea plant Camellia sinensis to better understand its production of flavonoids, theanine, and … more »

Posted in Citation | Tagged , , | Comments Off on Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis

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