Results 111 to 120 of about 567,059 (348)

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

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

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

YAP1::TFE3 mediates endothelial‐to‐mesenchymal plasticity in epithelioid hemangioendothelioma

Molecular Oncology, EarlyView.
The YAP1::TFE3 fusion protein drives endothelial‐to‐mesenchymal transition (EndMT) plasticity, resulting in the loss of endothelial characteristics and gain of mesenchymal‐like properties, including resistance to anoikis, increased migratory capacity, and loss of contact growth inhibition in endothelial cells.
Ant Murphy, Samuel Hartzler, Paula A. Vargas Carranza, Shyaman Jayasundara, Madison E. Yates, Nimod D. Janson, Bozhi Liu, Annaleigh Benton, Majid Kazemian, Jason A. Hanna   +9 more
wiley   +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

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

Simulating multiple faceted variability in single cell RNA sequencing. [PDF]

, 2019
The abundance of new computational methods for processing and interpreting transcriptomes at a single cell level raises the need for in silico platforms for evaluation and validation.
Xu, Chenling, Yosef, Nir, Zhang, Xiuwei
core  

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

Emerging role of ARHGAP29 in melanoma cell phenotype switching

Molecular Oncology, EarlyView.
This study gives first insights into the role of ARHGAP29 in malignant melanoma. ARHGAP29 was revealed to be connected to tumor cell plasticity, promoting a mesenchymal‐like, invasive phenotype and driving tumor progression. Further, it modulates cell spreading by influencing RhoA/ROCK signaling and affects SMAD2 activity. Rho GTPase‐activating protein
Beatrice Charlotte Tröster, Melanie Kappelmann‐Fenzl, Anja Katrin Bosserhoff, Nicole Rachinger   +3 more
wiley   +1 more source

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