Results 31 to 40 of about 38,805 (217)

RNA-Seq Assembly – Are We There Yet? [PDF]

Frontiers in Plant Science, 2012
Transcriptomic sequence resources represent invaluable assets for research, in particular for non-model species without a sequenced genome. To date, the Next Generation Sequencing technologies 454/Roche and Illumina have been used to generate transcriptome sequence databases by mRNA-Seq for more than fifty different plant species.
Schliesky, Simon, Gowik, Udo, Weber, Andreas P. M., Bräutigam, Andrea   +3 more
openaire   +4 more sources

Supersplat—spliced RNA-seq alignment [PDF]

Bioinformatics, 2010
Abstract Motivation: High-throughput sequencing technologies have recently made deep interrogation of expressed transcript sequences practical, both economically and temporally. Identification of intron/exon boundaries is an essential part of genome annotation, yet remains a challenge.
Douglas W. Bryant Jr., Rongkun Shen, Henry D. Priest, Weng-Keen Wong, Todd C. Mockler   +4 more
openaire   +2 more sources

Improving RNA-Seq Precision with MapAl [PDF]

Frontiers in Genetics, 2012
With currently available RNA-Seq pipelines, expression estimates for most genes are very noisy. We here introduce MapAl, a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. In the post-processing of RNA-Seq reads, it incorporates gene models already at the stage of read alignment, increasing the number ...
Paweł P Łabaj, Bryan E Linggi, H Steven eWiley, David P Kreil, David P Kreil   +4 more
openaire   +3 more sources

Integrated Analysis of Single-Cell RNA-Seq and Bulk RNA-Seq Combined with Multiple Machine Learning Identified a Novel Immune Signature in Diabetic Nephropathy

Diabetes, Metabolic Syndrome and Obesity, 2023
Yue-Ling Peng,1 Yan Zhang,1 Lin Pang,2 Ya-Fang Dong,3 Mu-Ye Li,4 Hui Liao,5 Rong-Shan Li1 1Department of Nephrology, Shanxi Provincial People’s Hospital (Fifth Hospital of Shanxi Medical University), Taiyuan, People’s Republic of China; 2Department of ...
Peng YL, Zhang Y, Pang L, Dong YF, Li MY, Liao H, Li RS   +6 more
doaj  

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism

Frontiers in Bioinformatics, 2023
Introduction: The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems.
Ryan S. McClure, Yvonne Rericha, Katrina M. Waters, Katrina M. Waters, Robyn L. Tanguay   +4 more
doaj   +1 more source

RNA‐Seq for Bacterial Gene Expression [PDF]

Current Protocols in Nucleic Acid Chemistry, 2018
AbstractRNA sequencing (RNA‐seq) has become the preferred method for global quantification of bacterial gene expression. With the continued improvements in sequencing technology and data analysis tools, the most labor‐intensive and expensive part of an RNA‐seq experiment is the preparation of sequencing libraries, which is also essential for the ...
Poulsen, Line Dahl, Vinther, Jeppe
openaire   +3 more sources

Comprehensive Assessments of RNA-seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine

Pharmaceutics, 2016
Studies on gene expression in response to therapy have led to the discovery of pharmacogenomics biomarkers and advances in precision medicine. Whole transcriptome sequencing (RNA-seq) is an emerging tool for profiling gene expression and has received ...
Joshua Xu, Binsheng Gong, Leihong Wu, Shraddha Thakkar, Huixiao Hong, Weida Tong   +5 more
doaj   +1 more source

RNA-seq

青角鹧鸪鸡肺部转录组
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Prime-seq, efficient and powerful bulk RNA sequencing

Genome Biology, 2022
Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method.
Aleksandar Janjic, Lucas E. Wange, Johannes W. Bagnoli, Johanna Geuder, Phong Nguyen, Daniel Richter, Beate Vieth, Binje Vick, Irmela Jeremias, Christoph Ziegenhain, Ines Hellmann, Wolfgang Enard   +11 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   +1 more source