RNA-Seq Blog Transcriptome Research & Industry News
In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable...
Read More »SAVER – gene expression recovery for single-cell RNA sequencing
Gene expression distribution deconvolution in single-cell RNA sequencing
Single-cell RNA sequencing (scRNA-seq) enables the quantification of each gene’s expression distribution across cells, thus allowing the assessment of the...
Read More »scRNA-Seq reveals that previous studies in blood have largely failed to capture the major component of HIV-specific CD8+ T cell responses in lymphoid tissues
Current paradigms of CD8+ T cell–mediated protection in HIV infection center almost exclusively on studies of peripheral blood, which is thought to provide a window into immune activity at the predominant sites of viral replication in lymphoid tissues (LTs). Through ...
Read More »SPAR – small RNA-seq portal for analysis of sequencing experiments
The introduction of new high-throughput small RNA sequencing protocols that generate large-scale genomics datasets along with increasing evidence of the significant regulatory roles of small non-coding RNAs (sncRNAs) have highlighted the urgent need for...
Read More »Integrative deep models for alternative splicing
Advancements in sequencing technologies have highlighted the role of alternative splicing (AS) in increasing transcriptome complexity. This role of AS, combined with the relation of aberrant splicing to malignant states, motivated two streams of research, experimental and computational. The first ...
Read More »Cross-Platform Normalization Enables Machine Learning Model Training On Microarray And RNA-Seq Data Simultaneously
Large compendia of gene expression data have proven valuable for the discovery of novel biological relationships. The majority of available RNA assays are run on microarray, while RNA-seq is becoming the platform of choice for new experiments. The data structure ...
Read More »Modeling allele-specific gene expression by single-cell RNA sequencing
Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing (scRNA-seq) allows the comparison of expression distribution between the two alleles of a diploid organism and thus the characterization of allele-specific bursting. ...
Read More »Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
A key component in many RNA-Seq based studies is the production of multiple replicates for varying experimental conditions. Such replicates allow to capture underlying biological variability and control for experimental ones. However, during data production researchers often lack clear definitions ...
Read More »Comprehensive benchmarking of RNA-Seq aligners
Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. Researchers from the University of ...
Read More »A new University of Pennsylvania effort is bringing RNA sequencing into high school classrooms through a free online resource
The goal is to make it easier for science teachers to incorporate the latest advances in science into their curricula. The initiative, Discovering the Genome, was spearheaded by Kristin Field, director of programs at Penn’s Nano/Bio Interface Center, and Junhyong ...
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