Finding the active genes in deep RNA-seq gene expression studies

T Hart, HK Komori, S LaMere, K Podshivalova… - BMC genomics, 2013 - Springer
Background Early application of second-generation sequencing technologies to transcript
quantitation (RNA-seq) has hinted at a vast mammalian transcriptome, including transcripts …

Progress in prokaryotic transcriptomics

MJ Filiatrault - Current opinion in microbiology, 2011 - Elsevier
Genome-wide expression studies transformed the field of transcriptomics and made it
feasible to study global gene expression in extraordinary detail. These new methods have …

Variability of venom components in immune suppressive parasitoid wasps: from a phylogenetic to a population approach

D Colinet, H Mathe-Hubert, R Allemand, JL Gatti… - Journal of Insect …, 2013 - Elsevier
Endoparasitoid wasps develop at the expense of other insects, leading to their death. Eggs
deposited inside the host body induce an immune response, which results in the formation …

Whole-transcriptome RNAseq analysis from minute amount of total RNA

MA Tariq, HJ Kim, O Jejelowo… - Nucleic acids …, 2011 - academic.oup.com
RNA sequencing approaches to transcriptome analysis require a large amount of input total
RNA to yield sufficient mRNA using either poly-A selection or depletion of rRNA. This feature …

SERE: single-parameter quality control and sample comparison for RNA-Seq

SK Schulze, R Kanwar, M Gölzenleuchter… - BMC genomics, 2012 - Springer
Background Assessing the reliability of experimental replicates (or global alterations
corresponding to different experimental conditions) is a critical step in analyzing RNA-Seq …

A cost-effective RNA sequencing protocol for large-scale gene expression studies

Z Hou, P Jiang, SA Swanson, AL Elwell, BKS Nguyen… - Scientific reports, 2015 - nature.com
RNA sequencing has increasingly become an indispensable tool for biological research.
While sequencing costs have fallen dramatically in recent years, the current cost of RNA …

RNA-seq based transcriptomic analysis of single bacterial cells

J Wang, L Chen, Z Chen, W Zhang - Integrative Biology, 2015 - academic.oup.com
Gene-expression heterogeneity among individual cells determines the fate of a bacterial
population. Here we report the first bacterial single-cell RNA sequencing (RNA-seq), BaSiC …

Functionally diverse dendritic mRNAs rapidly associate with ribosomes following a novel experience

JA Ainsley, L Drane, J Jacobs, KA Kittelberger… - Nature …, 2014 - nature.com
The subcellular localization and translation of messenger RNA (mRNA) supports functional
differentiation between cellular compartments. In neuronal dendrites, local translation of …

Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation

HK Komori, T Hart, SA LaMere, PV Chew… - The Journal of …, 2015 - journals.aai.org
Memory T cells are primed for rapid responses to Ag; however, the molecular mechanisms
responsible for priming remain incompletely defined. CpG methylation in promoters is an …

H3K27 methylation dynamics during CD4 T cell activation: regulation of JAK/STAT and IL12RB2 expression by JMJD3

SA LaMere, RC Thompson, X Meng… - The Journal of …, 2017 - journals.aai.org
The changes to the epigenetic landscape in response to Ag during CD4 T cell activation
have not been well characterized. Although CD4 T cell subsets have been mapped globally …