Literature DB >> 34302660

RNA-Sequencing Analysis of Differentially Expressed Genes in Human iPSC-Derived Cardiomyocytes.

Chikako Okubo1, Megumi Narita2, Takuya Yamamoto3,4,5,6, Yoshinori Yoshida7.   

Abstract

RNA sequencing profiles and characterizes cell and tissue samples, giving important insights into molecular mechanisms. Such data is imperative for cardiomyocytes derived from induced pluripotent stem cells (iPSC-CMs) and used in related translational and basic research. Here we provide reliable protocols to extract differentially expressed genes in iPSC-CMs with RNA sequencing.
© 2021. Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Gene expression; Genome-wide analysis; Molecular biology; Next-generation sequencer; RNA sequencing; Transcriptome

Year:  2021        PMID： 34302660     DOI： 10.1007/978-1-0716-1484-6_19

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  28 in total

1.  RSeQC: quality control of RNA-seq experiments.

Authors:  Liguo Wang; Shengqin Wang; Wei Li
Journal:  Bioinformatics       Date:  2012-06-27       Impact factor: 6.937

2.  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

3.  Fast gapped-read alignment with Bowtie 2.

Authors:  Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2012-03-04       Impact factor: 28.547

4.  Sensitive high-performance liquid chromatographic determination of ionic drugs in biological fluids with short-wavelength ultraviolet detection using column switching combined with ion-pair chromatography: application to basic compounds.

Authors:  K Yamashita; M Motohashi; T Yashiki
Journal:  J Chromatogr       Date:  1989-02-24

5.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.

Authors:  Michael I Love; Wolfgang Huber; Simon Anders
Journal:  Genome Biol       Date:  2014       Impact factor: 13.583

6.  HTSeq--a Python framework to work with high-throughput sequencing data.

Authors:  Simon Anders; Paul Theodor Pyl; Wolfgang Huber
Journal:  Bioinformatics       Date:  2014-09-25       Impact factor: 6.937

7.  Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences.

Authors:  Anqi Zhu; Joseph G Ibrahim; Michael I Love
Journal:  Bioinformatics       Date:  2019-06-01       Impact factor: 6.937

8.  GtRNAdb: a database of transfer RNA genes detected in genomic sequence.

Authors:  Patricia P Chan; Todd M Lowe
Journal:  Nucleic Acids Res       Date:  2008-11-04       Impact factor: 16.971

9.  GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes.

Authors:  Patricia P Chan; Todd M Lowe
Journal:  Nucleic Acids Res       Date:  2015-12-15       Impact factor: 16.971

10.  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
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  1 in total

1.  A stress-reduced passaging technique improves the viability of human pluripotent cells.

Authors:  Kazutoshi Takahashi; Chikako Okubo; Michiko Nakamura; Mio Iwasaki; Yuka Kawahara; Tsuyoshi Tabata; Yousuke Miyamoto; Knut Woltjen; Shinya Yamanaka
Journal:  Cell Rep Methods       Date:  2022-01-24
  1 in total

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