Bacterial regulatory RNA : methods and protocols / edited by Véronique Arluison, Claudio Valverde.

Contributor(s): Arluison, Veronique [editor.] | Valverde, Claudio [editor.]
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 1737.Publisher: New York, NY : Humana Press ; Springer, [2018]Copyright date: ©2018Description: 1 online resource (xii, 395 pages) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9781493976348; 1493976346; 9781493976331; 1493976338Subject(s): RNA -- Laboratory manuals | RNA | RNA | RNA, BacterialGenre/Form: Electronic books. | Laboratory Manual. | Laboratory manuals. Additional physical formats: Print version:: No titleDDC classification: 572.8/8 LOC classification: QH454 | .B338 2018Online resources: Click here to access online
Contents:
Workflow for a computational analysis of an sRNA candidate in bacteria / Patrick R. Wright and Jens Georg -- Guidelines for inferring and characterizing a family of bacterial trans-acting small noncoding RNAs / Antonio Lagares Jr. and Claudio Valverde -- Bioinformatic approach for prediction of CsrA/RsmA-regulating small RNAs in bacteria / Carl T. Fakhry, Kourosh Zarringhalam, and Rahul V. Kulkarni -- Host-pathogen transcriptomics by dual RNA-Seq / Alexander J. Westermann and Jörg Vogel -- Identification of new bacterial small RNA targets using MS2 affinity purification coupled to RNA sequencing / Marie-Claude Carrier, Guillaume Laliberté, and Eric Massé -- Assessment of external guide sequences' (EGS) efficiency as inducers of RNase P-mediated cleavage of mRNA target molecules / Saumya Jani, Alexis Jackson, Carol Davies-Sala, Kevin Chiem, Alfonso Soler-Bistué, Angeles Zorreguieta, and Marcelo E. Tolmasky -- Evaluating the effect of small RNAs and associated chaperones on rho-dependent termination of transcription in vitro / Cédric Nadiras, Annie Schwartz, Mildred Delaleau, and Marc Boudvillain -- Mapping changes in cell surface protein expression through selective labeling of live cells / Pierre Fechter -- Fluorescence-based methods for characterizing RNA interactions in vivo / Abigail N. Leistra, Mia K. Mihailovic, and Lydia M. Contreras -- Mutational analysis of sRNA-mRNA base pairing by electrophoretic mobility shift assay / Eva Maria Sternkopf Lillebæk and Birgitte Haahr Kallipolitis -- Integrated cell-free assay to study translation regulation by small bacterial noncoding RNAs / Erich Michel, Olivier Duss, and Frédéric H.-T. Allain -- Quantitative super-resolution imaging of small RNAs in Bacterial Cells / Seongjin Park, Magda Bujnowska, Eric L. McLean, and Jingyi Fei -- Extraction and analysis of RNA isolated from pure bacteria-derived outer membrane vesicles / Janine Habier, Patrick May, Anna Heintz-Buschart, Anubrata Ghosal, Anke K. Wienecke-Baldacchino, Esther N.M. Nolte-'t Hoen, Paul Wilmes, and Joëlle V. Fritz -- Absolute regulatory small noncoding RNA concentration and decay rates measurements in Escherichia coli / Florent Busi, Véronique Arluison, and Philippe Régnier -- High-resolution, high-throughput analysis of Hfq-binding sites using UV crosslinking and analysis of cDNA (CRAC) / Brandon Sy, Julia Wong, Sander Granneman, David Tollervey, David Gally, and Jai J. Tree -- Producing Hfq/Sm proteins and sRNAs for structural and biophysical studies of ribonucleoprotein assembly / Kimberly A. Stanek and Cameron Mura -- Single-molecule FRET assay to observe the activity of proteins involved in RNA/RNA annealing / Thierry Bizebard, Véronique Arluison, and Ulrich Bockelmann -- Techniques to analyze sRNA protein cofactor self-assembly in vitro / David Partouche, Antoine Malabirade, Thomas Bizien, Marisela Velez, Sylvain Trépout, Sergio Marco, Valeria Militello, Christophe Sandt, Frank Wien, and Véronique Arluison -- Sequence-specific affinity chromatography of bacterial small regulatory RNA-binding proteins from bacterial cells / Jonathan Gans, Jonathan Osborne, Juliet Cheng, Louise Djapgne, and Amanda G. Oglesby-Sherrouse -- Identification of small RNA-protein partners in plant symbiotic bacteria / Marta Robledo, Ana M. Matia-González, Natalia I. García-Tomsig, and José I. Jiménez-Zurdo -- Modular genetic system for high-throughput profiling and engineering of multi-target small RNAs / Samuel D. Stimple, Ashwin Lahiry, Joseph E. Taris, David W. Wood, and Richard A. Lease.
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Includes bibliographical references and index.

Workflow for a computational analysis of an sRNA candidate in bacteria / Patrick R. Wright and Jens Georg -- Guidelines for inferring and characterizing a family of bacterial trans-acting small noncoding RNAs / Antonio Lagares Jr. and Claudio Valverde -- Bioinformatic approach for prediction of CsrA/RsmA-regulating small RNAs in bacteria / Carl T. Fakhry, Kourosh Zarringhalam, and Rahul V. Kulkarni -- Host-pathogen transcriptomics by dual RNA-Seq / Alexander J. Westermann and Jörg Vogel -- Identification of new bacterial small RNA targets using MS2 affinity purification coupled to RNA sequencing / Marie-Claude Carrier, Guillaume Laliberté, and Eric Massé -- Assessment of external guide sequences' (EGS) efficiency as inducers of RNase P-mediated cleavage of mRNA target molecules / Saumya Jani, Alexis Jackson, Carol Davies-Sala, Kevin Chiem, Alfonso Soler-Bistué, Angeles Zorreguieta, and Marcelo E. Tolmasky -- Evaluating the effect of small RNAs and associated chaperones on rho-dependent termination of transcription in vitro / Cédric Nadiras, Annie Schwartz, Mildred Delaleau, and Marc Boudvillain -- Mapping changes in cell surface protein expression through selective labeling of live cells / Pierre Fechter -- Fluorescence-based methods for characterizing RNA interactions in vivo / Abigail N. Leistra, Mia K. Mihailovic, and Lydia M. Contreras -- Mutational analysis of sRNA-mRNA base pairing by electrophoretic mobility shift assay / Eva Maria Sternkopf Lillebæk and Birgitte Haahr Kallipolitis -- Integrated cell-free assay to study translation regulation by small bacterial noncoding RNAs / Erich Michel, Olivier Duss, and Frédéric H.-T. Allain -- Quantitative super-resolution imaging of small RNAs in Bacterial Cells / Seongjin Park, Magda Bujnowska, Eric L. McLean, and Jingyi Fei -- Extraction and analysis of RNA isolated from pure bacteria-derived outer membrane vesicles / Janine Habier, Patrick May, Anna Heintz-Buschart, Anubrata Ghosal, Anke K. Wienecke-Baldacchino, Esther N.M. Nolte-'t Hoen, Paul Wilmes, and Joëlle V. Fritz -- Absolute regulatory small noncoding RNA concentration and decay rates measurements in Escherichia coli / Florent Busi, Véronique Arluison, and Philippe Régnier -- High-resolution, high-throughput analysis of Hfq-binding sites using UV crosslinking and analysis of cDNA (CRAC) / Brandon Sy, Julia Wong, Sander Granneman, David Tollervey, David Gally, and Jai J. Tree -- Producing Hfq/Sm proteins and sRNAs for structural and biophysical studies of ribonucleoprotein assembly / Kimberly A. Stanek and Cameron Mura -- Single-molecule FRET assay to observe the activity of proteins involved in RNA/RNA annealing / Thierry Bizebard, Véronique Arluison, and Ulrich Bockelmann -- Techniques to analyze sRNA protein cofactor self-assembly in vitro / David Partouche, Antoine Malabirade, Thomas Bizien, Marisela Velez, Sylvain Trépout, Sergio Marco, Valeria Militello, Christophe Sandt, Frank Wien, and Véronique Arluison -- Sequence-specific affinity chromatography of bacterial small regulatory RNA-binding proteins from bacterial cells / Jonathan Gans, Jonathan Osborne, Juliet Cheng, Louise Djapgne, and Amanda G. Oglesby-Sherrouse -- Identification of small RNA-protein partners in plant symbiotic bacteria / Marta Robledo, Ana M. Matia-González, Natalia I. García-Tomsig, and José I. Jiménez-Zurdo -- Modular genetic system for high-throughput profiling and engineering of multi-target small RNAs / Samuel D. Stimple, Ashwin Lahiry, Joseph E. Taris, David W. Wood, and Richard A. Lease.

Online resource; title from PDF title page (SpringerProtocol, viewed February 27, 2018).

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