Literature DB >> 32729748

Incomplete removal of ribosomal RNA can affect chromatin RNA-seq data analysis.

Michael Tellier1, Shona Murphy1.   

Abstract

Entities:  

Keywords:  Chromatin RNA-seq; rRNA; ribosomal RNA; transcription

Mesh：

Substances：

Year:  2020        PMID： 32729748      PMCID： PMC7714438          DOI： 10.1080/21541264.2020.1794491

Source DB:  PubMed          Journal:  Transcription        ISSN： 2154-1272


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  14 in total

1.  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

2.  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

3.  IVT-seq reveals extreme bias in RNA sequencing.

Authors:  Nicholas F Lahens; Ibrahim Halil Kavakli; Ray Zhang; Katharina Hayer; Michael B Black; Hannah Dueck; Angel Pizarro; Junhyong Kim; Rafael Irizarry; Russell S Thomas; Gregory R Grant; John B Hogenesch
Journal:  Genome Biol       Date:  2014-06-30       Impact factor: 13.583

4.  Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing.

Authors:  Jung-Hyun Kim; Alexander T Dilthey; Ramaiah Nagaraja; Hee-Sheung Lee; Sergey Koren; Dawood Dudekula; William H Wood Iii; Yulan Piao; Aleksey Y Ogurtsov; Koichi Utani; Vladimir N Noskov; Svetlana A Shabalina; David Schlessinger; Adam M Phillippy; Vladimir Larionov
Journal:  Nucleic Acids Res       Date:  2018-07-27       Impact factor: 16.971

5.  Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction.

Authors:  Zachary T Herbert; Jamie P Kershner; Vincent L Butty; Jyothi Thimmapuram; Sulbha Choudhari; Yuriy O Alekseyev; Jun Fan; Jessica W Podnar; Edward Wilcox; Jenny Gipson; Allison Gillaspy; Kristen Jepsen; Sandra Splinter BonDurant; Krystalynne Morris; Maura Berkeley; Ashley LeClerc; Stephen D Simpson; Gary Sommerville; Leslie Grimmett; Marie Adams; Stuart S Levine
Journal:  BMC Genomics       Date:  2018-03-15       Impact factor: 3.969

6.  A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes.

Authors:  Joshua D Eaton; Laura Francis; Lee Davidson; Steven West
Journal:  Genes Dev       Date:  2019-12-05       Impact factor: 11.361

7.  A Sequel to Sanger: amplicon sequencing that scales.

Authors:  Paul D N Hebert; Thomas W A Braukmann; Sean W J Prosser; Sujeevan Ratnasingham; Jeremy R deWaard; Natalia V Ivanova; Daniel H Janzen; Winnie Hallwachs; Suresh Naik; Jayme E Sones; Evgeny V Zakharov
Journal:  BMC Genomics       Date:  2018-03-27       Impact factor: 3.969

8.  Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters.

Authors:  Yun Chen; Athma A Pai; Jan Herudek; Michal Lubas; Nicola Meola; Aino I Järvelin; Robin Andersson; Vicent Pelechano; Lars M Steinmetz; Torben Heick Jensen; Albin Sandelin
Journal:  Nat Genet       Date:  2016-07-25       Impact factor: 38.330

9.  Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence.

Authors:  Takayuki Nojima; Michael Tellier; Jonathan Foxwell; Claudia Ribeiro de Almeida; Sue Mei Tan-Wong; Somdutta Dhir; Gwendal Dujardin; Ashish Dhir; Shona Murphy; Nick J Proudfoot
Journal:  Mol Cell       Date:  2018-11-15       Impact factor: 17.970

10.  R-Loops Promote Antisense Transcription across the Mammalian Genome.

Authors:  Sue Mei Tan-Wong; Somdutta Dhir; Nick J Proudfoot
Journal:  Mol Cell       Date:  2019-10-31       Impact factor: 17.970
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  1 in total

1.  CAPTURE of the Human U2 snRNA Genes Expands the Repertoire of Associated Factors.

Authors:  Joana Guiro; Mathias Fagbemi; Michael Tellier; Justyna Zaborowska; Stephanie Barker; Marjorie Fournier; Shona Murphy
Journal:  Biomolecules       Date:  2022-05-14
  1 in total

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