Results 11 to 20 of about 536,139 (245)

Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. [PDF]

, 2015
RNA-seq has become a popular technology for studying genetic variation of pre-mRNA alternative splicing. Commonly used RNA-seq aligners rely on the consensus splice site dinucleotide motifs to map reads across splice junctions.
Bahrami-Samani, Emad, Lu, Zhi-Xiang, Park, Juw Won, Stein, Shayna, Xing, Yi   +4 more
core   +11 more sources

Detecting differential usage of exons from RNA-seq data [PDF]

, 2012
RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires comparisons between treatments, tissues or conditions.
Simon Anders, Alejandro Reyes, Wolfgang Huber   +2 more
openalex   +6 more sources

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   +5 more sources

Holistic Optimization of Bioinformatic Analysis Pipeline for Detection and Quantification of 2′-O-Methylations in RNA by RiboMethSeq

Frontiers in Genetics, 2020
A major trend in the epitranscriptomics field over the last 5 years has been the high-throughput analysis of RNA modifications by a combination of specific chemical treatment(s), followed by library preparation and deep sequencing.
Florian Pichot, Florian Pichot, Florian Pichot, Virginie Marchand, Lilia Ayadi, Lilia Ayadi, Valérie Bourguignon-Igel, Valérie Bourguignon-Igel, Mark Helm, Yuri Motorin, Yuri Motorin   +10 more
doaj   +1 more source

Integrated analysis of single‐cell RNA‐seq dataset and bulk RNA‐seq dataset constructs a prognostic model for predicting survival in human glioblastoma

Brain and Behavior, 2022
Background Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. For patients with GBM, the median overall survival (OS) is 14.6 months and the 5‐year survival rate is 7.2%. It is imperative to develop a reliable model to predict
Wenwen Lai, Defu Li, Jie Kuang, Libin Deng, Quqin Lu   +4 more
doaj   +1 more source

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis [version 4; peer review: 2 approved, 1 not approved]

F1000Research, 2020
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be cumbersome ...
Syed Hussain Ather, Olaitan Igbagbo Awe, Thomas J. Butler, Tamiru Denka, Stephen Andrew Semick, Wanhu Tang, Ben Busby   +6 more
doaj   +1 more source

Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data

BMC Genomics, 2022
Background Circular RNA (circRNA), a class of RNA molecule with a loop structure, has recently attracted researchers due to its diverse biological functions and potential biomarkers of human diseases.
Manh Hung Nguyen, Ha-Nam Nguyen, Trung Nghia Vu   +2 more
doaj   +1 more source

A map of bat virus receptors derived from single-cell multiomics

Scientific Data, 2022
Measurement(s) RNA-seq gene expression profiling assay • ATAC-Seq Technology Type(s) RNA-seq of coding RNA from single cells • Single cell ATAC-seq (cell index) Sample Characteristic - Organism Rhinolophus ...
Tianhang Lv, Xiaoshan Wang, Chao Yu, Zhifeng Wang, Rong Xiang, Linmiao Li, Yue Yuan, Yuhang Wang, Xiaoyu Wei, Yeya Yu, Xiangyang He, Libiao Zhang, Qiuting Deng, Peiying Wu, Yong Hou, Jinping Chen, Chuanyu Liu, Gary Wong, Longqi Liu   +18 more
doaj   +1 more source

Long non-coding RNA and circular RNA and coding RNA profiling of plasma exosomes of osteosarcoma by RNA seq

Scientific Data, 2023
Osteosarcoma (OS) is a primary bone tumor with high malignancy and the mechanism of hematogenous metastasis in OS is still not clear. The plasma exosomes derived from osteosarcoma play a key role in the process of tumor metastasis.
Yun Liu, Haijun Tang, Chong Li, Nenggan Huang, Jifeng Miao, Lin Chen, Kai Luo, Feicui Li, Shangyu Liu, Shijie Liao, Wenyu Feng, Xinli Zhan, Tianyu Xie, Wei Tang, Qingjun Wei, Jili Lu   +15 more
doaj   +1 more source

Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies

BMC Genomics, 2023
The Iso-Seq method of full-length cDNA sequencing is suitable to quantify differentially expressed genes (DEGs), transcripts (DETs) and transcript usage (DTU).
Yan Ren, Elizabeth Tseng, Timothy P. L. Smith, Stefan Hiendleder, John L. Williams, Wai Yee Low   +5 more
doaj   +1 more source