Article citationsMore>>
G. Giannoukos, D. Ciulla, K. Huang, B. Haas, J. Izard, J. Levin, J. Livny, A. Earl, D. Gevers, D. Ward, C. Nusbaum, B. Birren and A. Gnirke, “Efficient and Robust RNA-seq Process for Cultured Bacteria and Complex Community Transcriptomes,” Genome Biology, Vol. 13, 2012, p. r23.
http://dx.doi.org/10.1186/gb-2012-13-3-r23
has been cited by the following article:
-
TITLE:
Evaluation of Ribosomal RNA Removal Protocols for Salmonella RNA-Seq Projects
AUTHORS:
Arvind A. Bhagwat, Z. Irene Ying, Allen Smith
KEYWORDS:
Ribosomal RNA Depletion; Bacterial NextGen Sequencing; Food Borne Pathogen RNA Sequencing
JOURNAL NAME:
Advances in Microbiology,
Vol.4 No.1,
January
16,
2014
ABSTRACT:
Next generation sequencing is a powerful technology
whose application in sequencing entire RNA populations (RNA-Seq) of food-borne
pathogens will provide valuable insights. A problem unique to prokaryotic
RNA-Seq is removal of ribosomal RNA. Unlike eukaryotic messenger RNA (mRNA),
bacterial mRNA species are devoid of polyadenylation at the 3’-end and thus the
approach of affinity enrichment of mRNA using oligo-dT probes is not an option.
Among several approaches to enriching mRNA molecules, removal of ribosomal RNA
(rRNA) by subtractive hybridization has been widely used. This approach is a
single-step procedure for which several rRNA-depletion kits are commercially
available. We evaluated three commercially available rRNA-depletion kits to
determine their respective efficiencies of rRNA removal from Salmonella enterica serovar Typhimurium
strain SL1344. The three protocols achieved varying degrees of rRNA depletion
and resulted in 8 to 1000-fold enrichment of mRNA. rRNA removal probes from two
of the three kits were unable to titrate out 23S rRNA species while removal of
16S rRNA was less efficient. The Ribo-Zero kit was most efficient in
eliminating 16S, 23S and 5S ribosomal RNA species from the transcriptome of S. enterica serovar Typhimurium strain
SL1344.
Related Articles:
-
Lengliz Hanene, Guerchi Meher, Carnus Marie France
-
Christian Willemse, Nader Soltani, Brendan Metzger, David C. Hooker, Amit J. Jhala, Darren E. Robinson, Peter H. Sikkema
-
Kouamé Hatrydt Guillaume Dimitri, Kissi Anzouan-Kacou Henriette Ya, Gogan Patricia, Bangoura Aboubacar Demba, Doffou Stanislas Adjeka, Mahassadi Kouame Alassan, Yao Bathaix Fulgence Mamert, Attia Alain Koffi
-
Mamert Fulgence Yao Bathaix, Dramane Soro, Aboubacar Demba Bangoura, Adjéka Stanislas Doffou, Siaka Koné, Ya Henriette Kissy, Dimitri Hartrydt Kouamé, Aoudi Ousmane Dé, Mahassadi Kouamé Alassane, Attia Koffi Alain, Aya Thérèse N’dri Yoman
-
Jai Dev Chandel, Nand Lal Singh