Literature DB >> 34950881

Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog.

Sini Ezer1,2, Masahito Yoshihara3, Shintaro Katayama1,2,3, Carsten Daub3,4, Hannes Lohi1,5,6, Kaarel Krjutskov7,8, Juha Kere1,2,3.   

Abstract

We have developed a protocol for barcoded cDNA libraries of 48 samples to study gene expression across tissues in the domestic dog, Canis familiaris, by modifying the Single-Cell Tagged Reverse Transcription (STRT) protocol (Islam et al., 2012, 2014). The cDNA reads represent mRNA 5' ends, enabling the study of transcription start sites (TSS). Our modifications include longer UMIs for molecular counting and Globin-Lock® to deplete globin mRNAs that are abundant in blood and blood-rich tissues dominating all reads.
© 2021 The Authors.

Entities:  

Keywords:  Bioinformatics; Gene Expression; Genomics; Model Organisms; Molecular Biology; RNAseq; Sequence analysis; Sequencing

Mesh：

Substances：

Year:  2021        PMID： 34950881      PMCID： PMC8672047          DOI： 10.1016/j.xpro.2021.100995

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


  11 in total

1.  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

2.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.

Authors:  Mihaela Pertea; Geo M Pertea; Corina M Antonescu; Tsung-Cheng Chang; Joshua T Mendell; Steven L Salzberg
Journal:  Nat Biotechnol       Date:  2015-02-18       Impact factor: 54.908

3.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.

Authors:  Daehwan Kim; Joseph M Paggi; Chanhee Park; Christopher Bennett; Steven L Salzberg
Journal:  Nat Biotechnol       Date:  2019-08-02       Impact factor: 54.908

4.  The Sequence Alignment/Map format and SAMtools.

Authors:  Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal:  Bioinformatics       Date:  2009-06-08       Impact factor: 6.937

5.  BEDTools: a flexible suite of utilities for comparing genomic features.

Authors:  Aaron R Quinlan; Ira M Hall
Journal:  Bioinformatics       Date:  2010-01-28       Impact factor: 6.937

6.  Highly multiplexed and strand-specific single-cell RNA 5' end sequencing.

Authors:  Saiful Islam; Una Kjällquist; Annalena Moliner; Pawel Zajac; Jian-Bing Fan; Peter Lönnerberg; Sten Linnarsson
Journal:  Nat Protoc       Date:  2012-04-05       Impact factor: 13.491

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.  Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods.

Authors:  Shintaro Katayama; Tiina Skoog; Cilla Söderhäll; Elisabet Einarsdottir; Kaarel Krjutškov; Juha Kere
Journal:  BMC Bioinformatics       Date:  2019-08-13       Impact factor: 3.169

9.  Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development.

Authors:  Virpi Töhönen; Shintaro Katayama; Liselotte Vesterlund; Eeva-Mari Jouhilahti; Mona Sheikhi; Elo Madissoon; Giuditta Filippini-Cattaneo; Marisa Jaconi; Anna Johnsson; Thomas R Bürglin; Sten Linnarsson; Outi Hovatta; Juha Kere
Journal:  Nat Commun       Date:  2015-09-11       Impact factor: 14.919

10.  Globin mRNA reduction for whole-blood transcriptome sequencing.

Authors:  Kaarel Krjutškov; Mariann Koel; Anne Mari Roost; Shintaro Katayama; Elisabet Einarsdottir; Eeva-Mari Jouhilahti; Cilla Söderhäll; Ülle Jaakma; Mario Plaas; Liselotte Vesterlund; Hannes Lohi; Andres Salumets; Juha Kere
Journal:  Sci Rep       Date:  2016-08-12       Impact factor: 4.379
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  2 in total

1.  Transient DUX4 expression in human embryonic stem cells induces blastomere-like expression program that is marked by SLC34A2.

Authors:  Masahito Yoshihara; Ida Kirjanov; Sonja Nykänen; Joonas Sokka; Jere Weltner; Karolina Lundin; Lisa Gawriyski; Eeva-Mari Jouhilahti; Markku Varjosalo; Mari H Tervaniemi; Timo Otonkoski; Ras Trokovic; Shintaro Katayama; Sanna Vuoristo; Juha Kere
Journal:  Stem Cell Reports       Date:  2022-06-30       Impact factor: 7.294

2.  Viral infection-related gene upregulation in monocytes in children with signs of β-cell autoimmunity.

Authors:  Milla Valta; Masahito Yoshihara; Elisabet Einarsdottir; Sirpa Pahkuri; Sini Ezer; Shintaro Katayama; Mikael Knip; Riitta Veijola; Jorma Toppari; Jorma Ilonen; Juha Kere; Johanna Lempainen
Journal:  Pediatr Diabetes       Date:  2022-04-25       Impact factor: 3.409
  2 in total

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