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
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
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
Micro RNA’s (miRNA’s) may help explain expression of multiple genes in Alzheimer’s Frontal Cortex
September 2017
Authors:
James Bennett and Paula Keeney
Info:
Scientists from Neurodegeneration Therapeutics used RNA-seq to compare microRNAs found in Alzheimer’s brain samples and controls. They identified 55 up-regulated genes and 191 down-regulated genes in the Alzheimer’s samples. PippinHT was used for small RNA size selection ahead of sequencing on an Illumina NextSeq500.
Citation:
Journal of Systems and Integrative Neuroscience
http://www.oatext.com/micro-rnas-mirnas-may-help-explain-expression-of-multiple-genes-in-alzheimers-frontal-cortex.php#Article