Results 61 to 70 of about 345,547 (215)

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM) [PDF]

Bioinformatics, 2011
Abstract Motivation: A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting ...
John B. Hogenesch, Gregory R. Grant, Angel Pizarro, Eric A. Pierce, Nicholas F. Lahens, Jonathan Schug, Brian P. Brunk, Christian J. Stoeckert, Michael H. Farkas   +8 more
openaire   +3 more sources

CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA Contamination in RNA-Seq Data

BioTech
RNA sequencing (RNA-seq) has become a standard method for profiling gene expression, yet genomic DNA (gDNA) contamination carried over to the sequencing library poses a significant challenge to data integrity.
Haibo Liu, Kai Hu, Kevin O’Connor, Michelle A. Kelliher, Lihua Julie Zhu   +4 more
doaj   +1 more source

A bifunctional snoRNA with separable activities in guiding rRNA 2’-O-methylation and scaffolding gametogenesis effectors

Nature Communications
Small nucleolar RNAs are non-coding transcripts that guide chemical modifications of RNA substrates and modulate gene expression at the epigenetic and post-transcriptional levels.
Estelle Leroy, Drice Challal, Stéphane Pelletier, Coralie Goncalves, Alexandra Menant, Virginie Marchand, Yan Jaszczyszyn, Erwin van Dijk, Delphine Naquin, Jessica Andreani, Yuri Motorin, Benoit Palancade, Mathieu Rougemaille   +12 more
doaj   +1 more source

Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action

Toxicology Reports, 2022
Formalin-fixed paraffin-embedded (FFPE) samples are the only remaining biological archive for many toxicological and clinical studies, yet their use in genomics has been limited due to nucleic acid damage from formalin fixation.
Michael D. Cannizzo, Charles E. Wood, Susan D. Hester, Leah C. Wehmas   +3 more
doaj  

SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology

Genome Biology, 2018
We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq).
Mahmoud N. Abdelmoez, Kei Iida, Yusuke Oguchi, Hidekazu Nishikii, Ryuji Yokokawa, Hidetoshi Kotera, Sotaro Uemura, Juan G. Santiago, Hirofumi Shintaku   +8 more
doaj   +1 more source

Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

BMC Genomics, 2018
Background RNA-seq and small RNA-seq are powerful, quantitative tools to study gene regulation and function. Common high-throughput sequencing methods rely on polymerase chain reaction (PCR) to expand the starting material, but not every molecule ...
Yu Fu, Pei-Hsuan Wu, Timothy Beane, Phillip D. Zamore, Zhiping Weng   +4 more
doaj   +1 more source

Integrated Analysis of Single-Cell RNA-seq and Bulk RNA-seq in the Identification of a Novel ceRNA Network and Key Biomarkers in Diabetic Kidney Disease

International Journal of General Medicine, 2022
Yuejun Wang,1 Mingming Zhao,2 Yu Zhang2 1Department of Nephrology, Zhejiang Aged Care Hospital, Hangzhou Normal University, Hangzhou, Zhejiang, People’s Republic of China; 2Department of Nephrology, Xiyuan Hospital, China Academy of Chinese Medical ...
Wang Y, Zhao M, Zhang Y
doaj  

The impact of quality filter for RNA-Seq

Gene, 2015
With the emergence of large-scale sequencing platforms since 2005, there has been a great revolution regarding methods for decoding DNA sequences, which have also affected quantitative and qualitative gene expression analyses through the RNA-Sequencing technique.
de Sá, Pablo H.C.G., Veras, Adonney A.O., Carneiro, Adriana R., Pinheiro, Kenny C., Pinto, Anne C., Soares, Siomar C., Schneider, Maria P.C., Azevedo, Vasco, Silva, Artur, Ramos, Rommel T.J.   +9 more
openaire   +3 more sources

DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data

Frontiers in Genetics, 2018
RNA sequencing (RNA-seq) has become a widely used technology for analyzing global gene-expression changes during certain biological processes. It is generally acknowledged that RNA-seq data displays equidispersion and overdispersion characteristics ...
Zhihua Gao, Zhihua Gao, Zhiying Zhao, Wenqiang Tang   +3 more
doaj   +1 more source

RNA-Seq Data: A Complexity Journey

Computational and Structural Biotechnology Journal, 2014
A paragraph from the highlights of "Transcriptomics: Throwing light on dark matter" by L. Flintoft (Nature Reviews Genetics 11, 455, 2010), says: "Reports over the past few years of extensive transcription throughout eukaryotic genomes have led to considerable excitement.
openaire   +4 more sources