Citations

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

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 an assembly with a contig N50 of 2.5 Mb. The high error rate was reduced by polishing with Illumina reads. The team enriched for long reads by using BluePippin to remove smaller fragments prior to sequencing.

Citation:
The Plant Cell
doi: 10.1105/tpc.17.00521

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A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value

October 2017

Authors:
Changsong Zou, Aojun Chen, Lihong Xiao, Heike Muller, et al.

Info:
Scientists deployed several sequencing platforms to characterize the genome of Chenopodium quinoa, an important and highly nutritious cereal crop. They analyzed the assembly to better understand the plant’s remarkable stress tolerance and its genomic evolution. SageELF was used to prepare DNA fractions for PCR-free library construction in an Illumina workflow.

Citation:
Cell Research (2017) 27, 1327–1340 (2017)
doi:10.1038/cr.2017.124

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Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

October 2017

Authors:
Malgorzata Komor, Thang Pham, Annemieke Hiemstra, Sander Piersma, et al.

Info:
In this paper, scientists from the Netherlands Cancer Institute, VU University Medical Center, and other institutions describe results from a new pipeline to detect differentially expressed protein isoforms. The method uses RNA sequencing and tandem mass spectrometry. In validation studies, the team used SageELF to separate library fractions into several size bins.

Citation:
Molecular & Cellular Proteomics 16,1850-1863
doi:10.1074/mcp.TIR117.000056

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

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 Illumina MiSeq and size selection with the BluePippin. Samples were typed in six different labs, demonstrating high accuracy and reproducibility of results.

Citation:
Human Immunology
Volume 78, Issue 10, Pages 642-648

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

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 than 1,200 differentially expressed genes between the samples. Sequencing was performed on an Illumina HiSeq 2500, with size selection conducted on BluePippin.

Citation:
Ann Dermatol. 2017 Oct;29(5):597-601
doi: 10.5021/ad.2017.29.5.597

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