Literature DB >> 33786463

Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging.

Xinyue Lu1, Qiuzhong Zhou2, Jin Liu3, Lei Sun2.   

Abstract

Comprehensive analyses of lncRNAs in aging have been lacking because previous studies have mainly focused on the protein-coding genes during aging. Here, we describe a protocol for the organism-wide analysis of murine lncRNAs during aging. We provide step-by-step instructions to identify lncRNAs that contribute to aging and to determine their underlying functions in each tissue. We further describe methods to compare the lncRNA expression patterns and dynamic changes among multiple tissues. For complete details on the use and execution of this protocol, please refer to Zhou et al. (2020).
© 2021 The Authors.

Entities:  

Keywords:  Genomics; RNAseq; Sequencing

Mesh：

Substances：

Year:  2021        PMID： 33786463      PMCID： PMC7994534          DOI： 10.1016/j.xpro.2021.100397

Source DB:  PubMed          Journal:  STAR Protoc        ISSN： 2666-1667


  12 in total

1.  clusterProfiler: an R package for comparing biological themes among gene clusters.

Authors:  Guangchuang Yu; Li-Gen Wang; Yanyan Han; Qing-Yu He
Journal:  OMICS       Date:  2012-03-28

2.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.

Authors:  Yang Liao; Gordon K Smyth; Wei Shi
Journal:  Bioinformatics       Date:  2013-11-13       Impact factor: 6.937

3.  STAR: ultrafast universal RNA-seq aligner.

Authors:  Alexander Dobin; Carrie A Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R Gingeras
Journal:  Bioinformatics       Date:  2012-10-25       Impact factor: 6.937

4.  De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development.

Authors:  Juan R Alvarez-Dominguez; Zhiqiang Bai; Dan Xu; Bingbing Yuan; Kinyui Alice Lo; Myeong Jin Yoon; Yen Ching Lim; Marko Knoll; Nikolai Slavov; Shuai Chen; Chen Peng; Harvey F Lodish; Lei Sun
Journal:  Cell Metab       Date:  2015-04-23       Impact factor: 27.287

5.  A scaling normalization method for differential expression analysis of RNA-seq data.

Authors:  Mark D Robinson; Alicia Oshlack
Journal:  Genome Biol       Date:  2010-03-02       Impact factor: 13.583

6.  The evolution of lncRNA repertoires and expression patterns in tetrapods.

Authors:  Anamaria Necsulea; Magali Soumillon; Maria Warnefors; Angélica Liechti; Tasman Daish; Ulrich Zeller; Julie C Baker; Frank Grützner; Henrik Kaessmann
Journal:  Nature       Date:  2014-01-19       Impact factor: 49.962

7.  MultiQC: summarize analysis results for multiple tools and samples in a single report.

Authors:  Philip Ewels; Måns Magnusson; Sverker Lundin; Max Käller
Journal:  Bioinformatics       Date:  2016-06-16       Impact factor: 6.937

8.  De novo reconstruction of human adipose transcriptome reveals conserved lncRNAs as regulators of brown adipogenesis.

Authors:  Chunming Ding; Yen Ching Lim; Sook Yoong Chia; Arcinas Camille Esther Walet; Shaohai Xu; Kinyui Alice Lo; Yanling Zhao; Dewen Zhu; Zhihui Shan; Qingfeng Chen; Melvin Khee-Shing Leow; Dan Xu; Lei Sun
Journal:  Nat Commun       Date:  2018-04-06       Impact factor: 14.919

9.  GENCODE reference annotation for the human and mouse genomes.

Authors:  Adam Frankish; Mark Diekhans; Anne-Maud Ferreira; Rory Johnson; Irwin Jungreis; Jane Loveland; Jonathan M Mudge; Cristina Sisu; James Wright; Joel Armstrong; If Barnes; Andrew Berry; Alexandra Bignell; Silvia Carbonell Sala; Jacqueline Chrast; Fiona Cunningham; Tomás Di Domenico; Sarah Donaldson; Ian T Fiddes; Carlos García Girón; Jose Manuel Gonzalez; Tiago Grego; Matthew Hardy; Thibaut Hourlier; Toby Hunt; Osagie G Izuogu; Julien Lagarde; Fergal J Martin; Laura Martínez; Shamika Mohanan; Paul Muir; Fabio C P Navarro; Anne Parker; Baikang Pei; Fernando Pozo; Magali Ruffier; Bianca M Schmitt; Eloise Stapleton; Marie-Marthe Suner; Irina Sycheva; Barbara Uszczynska-Ratajczak; Jinuri Xu; Andrew Yates; Daniel Zerbino; Yan Zhang; Bronwen Aken; Jyoti S Choudhary; Mark Gerstein; Roderic Guigó; Tim J P Hubbard; Manolis Kellis; Benedict Paten; Alexandre Reymond; Michael L Tress; Paul Flicek
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

10.  A Landscape of Murine Long Non-Coding RNAs Reveals the Leading Transcriptome Alterations in Adipose Tissue during Aging.

Authors:  Qiuzhong Zhou; Qianfen Wan; Yuxi Jiang; Jin Liu; Li Qiang; Lei Sun
Journal:  Cell Rep       Date:  2020-05-26       Impact factor: 9.423
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