Results 91 to 100 of about 588,819 (199)

Statistical Modeling of RNA-Seq Data

Statistical Science, 2011
Recently, ultra high-throughput sequencing of RNA (RNA-Seq) has been developed as an approach for analysis of gene expression. By obtaining tens or even hundreds of millions of reads of transcribed sequences, an RNA-Seq experiment can offer a comprehensive survey of the population of genes (transcripts) in any sample of interest.
Salzman, Julia, Jiang, Hui, Wong, Wing Hung   +2 more
openaire   +5 more sources

Barcode, UMI, Set format and BUStools [PDF]

, 2019
We introduce the Barcode-UMI-Set format (BUS) for representing pseudoalignments of reads from single-cell RNA-seq experiments. The format can be used with all single-cell RNA-seq technologies, and we show that BUS files can be efficiently generated ...
Melsted, Páll, Ntranos, Vasilis, Pachter, Lior   +2 more
core   +1 more source

From bench to bytes: a practical guide to RNA sequencing data analysis

Frontiers in Genetics
RNA sequencing (RNA-Seq) is a high-throughput sequencing approach that enables comprehensive quantification of transcriptomes at a genome-wide scale. As a result, RNA-Seq has become a routine component of molecular biology research, and more researchers ...
Prabin Dawadi, Bivek Pokharel, Anita Shrestha, Dikshya Niraula, Afifa Naeem, Sayaka Miura, Mishal Roy, Saroj Nepal   +7 more
doaj   +1 more source

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

Pan‐Cancer Single‐Nucleus Total RNA Sequencing Using snHH‐Seq

Advanced Science
Tumor heterogeneity and its drivers impair tumor progression and cancer therapy. Single‐cell RNA sequencing is used to investigate the heterogeneity of tumor ecosystems. However, most methods of scRNA‐seq amplify the termini of polyadenylated transcripts,
Haide Chen, Xiunan Fang, Jikai Shao, Qi Zhang, Liwei Xu, Jiaye Chen, Yuqing Mei, Mengmeng Jiang, Yuting Wang, Zhouyang Li, Zihang Chen, Yang Chen, Chengxuan Yu, Lifeng Ma, Peijing Zhang, Tianyu Zhang, Yuan Liao, Yuexiao Lv, Xueyi Wang, Lei Yang, Yuting Fu, Daobao Chen, Liming Jiang, Feng Yan, Wei Lu, Gao Chen, Huahao Shen, Jingjing Wang, Changchun Wang, Tingbo Liang, Xiaoping Han, Yongcheng Wang, Guoji Guo   +32 more
doaj   +1 more source

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

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

Quantitative RNA Analysis Using RNA-Seq

, 2019
High-throughput sequencing of cDNA copies of mRNA (RNA-seq) provides a digital readout of mRNA levels over several orders of magnitude, as well as mapping the transcripts to the nucleotide level. Here we describe two different RNA-seq approaches, including one that exploits the 39-nucleotide mini-exon or spliced leader (SL) sequence found at the 5' end
Myler, P. J., McDonald, Jacqueline A., Alcolea, Pedro J., Sur, Aakash   +3 more
openaire   +3 more sources

RNA sequencing and immunohistochemistry jointly improve tumor biomarker interpretation

Scientific Reports
This study aimed to assess the correlation between RNA sequencing (RNA-seq) and immunohistochemistry (IHC) in detecting key cancer biomarkers across solid tumors, and then, to establish RNA-seq thresholds that accurately reflect clinical IHC ...
Vladimir Kushnarev, Danil Stupichev, Suren Davitavyan, Kirill Kriukov, Basavaraja U. Shanthappa, Anna Butusova, Sofia Menshikova, Anna Belozerova, Anastasia Shvyrkova, Arina Tkachuk, Olga Khatenkova, Linda Balabanian, Ekaterina Postovalova, Jochen K. Lennerz, Funda Meric-Bernstam, Alexander Bagaev   +15 more
doaj   +1 more source

Poly(A) inclusive RNA isoform sequencing (PAIso−seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails

Nature Communications, 2019
The poly(A) tails on mRNA are vital for their function but it is difficult to map full-length sequences of mRNA isoforms with the entire poly(A) tails.
Yusheng Liu, Hu Nie, Hongxiang Liu, Falong Lu   +3 more
doaj   +1 more source