High-resolution transcriptome of human macrophages

M Beyer, MR Mallmann, J Xue, A Staratschek-Jox… - 2012 - journals.plos.org
Macrophages are dynamic cells integrating signals from their microenvironment to develop
specific functional responses. Although, microarray-based transcriptional profiling has …

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case …

I Nookaew, M Papini, N Pornputtapong… - Nucleic acids …, 2012 - academic.oup.com
RNA-seq, has recently become an attractive method of choice in the studies of
transcriptomes, promising several advantages compared with microarrays. In this study, we …

Integrating omic approaches for abiotic stress tolerance in soybean

R Deshmukh, H Sonah, G Patil, W Chen… - Frontiers in Plant …, 2014 - frontiersin.org
Soybean production is greatly influenced by abiotic stresses imposed by environmental
factors such as drought, water submergence, salt, and heavy metals. A thorough …

Navigating the pitfalls of mapping DNA and RNA modifications

Y Kong, EA Mead, G Fang - Nature Reviews Genetics, 2023 - nature.com
Chemical modifications to nucleic acids occur across the kingdoms of life and carry
important regulatory information. Reliable high-resolution mapping of these modifications is …

Principles of transcriptome analysis and gene expression quantification: an RNA‐seq tutorial

JBW Wolf - Molecular ecology resources, 2013 - Wiley Online Library
Genome‐wide analyses and high‐throughput screening was long reserved for biomedical
applications and genetic model organisms. With the rapid development of massively parallel …

Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs

Z Li, C Ender, G Meister, PS Moore… - Nucleic acids …, 2012 - academic.oup.com
Deep sequencing studies frequently identify small RNA fragments of abundant RNAs. These
fragments are thought to represent degradation products of their precursors. Using …

Transcriptional recording by CRISPR spacer acquisition from RNA

F Schmidt, MY Cherepkova, RJ Platt - Nature, 2018 - nature.com
The ability to record transcriptional events within a cell over time would help to elucidate
how molecular events give rise to complex cellular behaviours and states. However, current …

Introduction to single‐cell RNA sequencing

TK Olsen, N Baryawno - Current protocols in molecular biology, 2018 - Wiley Online Library
During the last decade, high‐throughput sequencing methods have revolutionized the entire
field of biology. The opportunity to study entire transcriptomes in great detail using RNA …

Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress

MV Gerashchenko, AV Lobanov… - Proceedings of the …, 2012 - National Acad Sciences
Information on unique and coordinated regulation of transcription and translation in
response to stress is central to the understanding of cellular homeostasis. Here we used …

Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

Z Jiang, X Zhou, R Li, JJ Michal, S Zhang… - Cellular and molecular …, 2015 - Springer
Whole transcriptome analysis plays an essential role in deciphering genome structure and
function, identifying genetic networks underlying cellular, physiological, biochemical and …