Single-cell RNA-Seq Gaining Steam

Single Cell Consensus Clustering (SC3) tool is more accurate and robust than existing methods (3/28/2017) - Wellcome Trust Sanger Institute scientists and their collaborators have developed a new analysis tool that was able to show, for the first time, which genes were expressed by individual cells in different genetic versions of a benign blood cancer. Single cell RNA sequencing can define cell types by revealing differences in the proteins produced by ...
rna-seq CountClust – visualizing the structure of RNA-seq expression data using grade of membership models (3/24/2017) - Grade of membership models, also known as “admixture models”, “topic models” or “Latent Dirichlet Allocation”, are a generalization of cluster models that allow each sample to have membership in multiple clusters. These models are widely used in population genetics to model admixed individuals who have ancestry from multiple “populations”, and in natural language processing to ...
rna-seq Upcoming Webinar – Optimizing Single-cell RNA-sequencing Workflows (3/22/2017) -  April 13, 2017 at 2:00 PM EST Hear from single cell sequencing experts, and learn about key technologies that promote cost savings while increasing the number of cells that you can include in your genetic analysis. Topics will include: • Applications of single-cell RNA-Seq • Optimization of sample prep workflows • Strategies for reagent handling ...
Single-cell RNA-Seq reveals subtypes of colorectal tumors (3/21/2017) - Combining single-cell genomics and computational techniques, a research team including Paul Robson, Ph.D., director of single-cell biology at The Jackson Laboratory (JAX), has defined cell-type composition of cancerous cells from 11 colorectal tumors, as well as adjacent noncancerous cells, a key to more targeted diagnosis and treatment. “Using single-cell signatures,” says JAX Research Scientist Elise ...
rna-seq powsim – Power analysis for bulk and single cell RNA-seq experiments (3/17/2017) - Simulations are essential to find the best compromise between statistical power and cost effectiveness, but also help with the interpretation of conducted RNA-seq experiments. For example, researchers often wonder why their results differ from previous studies, powsim helps here by allowing the researcher to assess whether this inconsistency could simply be due to chance because ...
rna-seq Single-cell RNA-Seq uncovers secrets of immune system’s response to malaria (3/13/2017) - Scientists have revealed for the first time how immature mouse immune cells, called T cells, choose which type of skills they will develop  to fight malaria infection. Reported today (3 March) in Science Immunology, researchers from the Wellcome Trust Sanger Institute, European Bioinformatics Institute and QIMR Berghofer Medical Research Institute, Australia, tracked individual T cells ...
Power analysis of single-cell RNA-sequencing experiments (3/9/2017) - Single-cell RNA sequencing (scRNA-seq) has become an established and powerful method to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and providing insights into developmental processes and transcriptional stochasticity. A key question is how the variety of available protocols compare in terms of their ability to detect and accurately quantify gene expression. Here, researchers ...
rna-seq Using Single Nucleotide Variations in Single-Cell RNA-Seq to Identify Tumor Subpopulations and Genotype-phenotype Linkage (3/9/2017) - Despite its popularity, characterization of subpopulations with transcript abundance is subject to significant amount of noise. Researchers at the University of Hawaii Cancer Center propose to use effective and expressed nucleotide variations (eeSNVs) from scRNA-seq as alternative features for tumor subpopulation identification. They developed a linear modeling framework SSrGE to link eeSNVs associated with gene expression. ...
rna-seq Single-Cell RNA Sequencing From Frozen Samples Feasible (3/3/2017) - GenomeWeb – A new study suggests the accuracy of transcriptional profiles produced from single cells does not seem to suffer significantly when samples are frozen beforehand. Researchers from Spain and Israel did RNA sequencing on nearly 700 individual cells nabbed from fresh samples and on more than 800 cells that had been frozen in the ...
Granatum – a graphical single-cell RNA-seq analysis pipeline for genomics scientists (2/24/2017) - Single-cell RNA sequencing (scRNA-seq) is an increasingly popular platform to study heterogeneity at the single cell level. Computational methods to process scRNA-seq have limited accessibility to bench scientists, as they require significant amount of bioinformatics skills. Researchers from the University of Hawaii at Manoa have developed Granatum, a web browser based scRNA-seq analysis pipeline to make ...

A slew of recent high profile papers and upcoming conferences highlight the growing interest in single-cell transcriptomics.