Review of selected publications citing Strand NGS

In 2015, we brought in many new features and improvements based on your requirements and feedback. We expanded the Strand NGS epigenomics toolkit by adding the MeDIP-Seq workflow in the v2.5 release. We also added new features like the alignment workflow and SV detection for split reads (watch the webinar), a browser-based copy number variation (CNV) view (watch the webinar), and correlation analysis. 2015 was also a year with some great publications that cited Avadis NGS and Strand NGS. Here is a small selection:

K-bZIP Mediated SUMO-2/3 Specific Modification on the KSHV Genome Negatively Regulates Lytic Gene Expression and Viral Reactivation (Wan-Shan Yang, et al.) published in PLoS Pathogens. The authors looked at ChIP-Seq data as well as RNA-Seq data to study the association of SUMO paralog genome modifications with KSHV (one of the seven known human oncoviruses) reactivation. Avadis NGS was used to align ChIP-Seq data to the KSHV genome build and to delineate the SUMO-1 and SUMO-2/3 binding patterns. RNA-Seq reads that did not align with hg19 were mapped with the KSHV genome in Avadis NGS and differential gene expression was determined based on sample wise transcript RPKM values reported by Avadis NGS and verified by RT-qPCR.

Novel roles for LIX1L in promoting cancer cell proliferation through ROS1-mediated LIX1L phosphorylation (Satoki Nakamura, et al.) published in Nature Scientific Reports. The authors report novel roles of Limb expression 1-like (LIX1L) in promoting cancer cell proliferation through ROS1- mediated LIX1L phosphorylation in oesophagus, gastric, breast, lung, thyroid, ovarian, kidney, liver, colon, prostate and pancreatic cancers. Strand NGS was used for alignment, filtering, quantification and statistical analysis of small RNA sequencing data, as well as prediction of miRNA targets.

Lysine-specific demethylase LSD2 suppresses lipid influx and metabolism in hepatic cells (Katsuya Nagaoka, et al.) published in Molecular and Cell Biology. The authors integrated transcriptomic, metabolomic and ChIP-Seq data to demonstrate the role of LSD2 in homeostatic control of the lipid metabolism in mouse hepatocytes. Avadis NGS was used to analyze and visualize the ChIP-Seq data.

Sex Specification and Heterogeneity of Primordial Germ Cells in Mice (Akihiko Sakashita,et al.) published in PLoS One. The authors report on female and male specific gene expression in the mouse primordial germ cells and the complex gene expression networks involved in PGC sex differentiation. RNA-Seq data analysis including quantification, normalization, fold change analysis and principal component analysis (bi-dimensional PCA) was performed in Strand NGS.

Congratulations to these authors and all the others who have seen their research efforts rewarded with a publication of their work.