Enhancer RNAs : methods and protocols / edited by Ulf Andesson Orom.

Contributor(s): Ørom, Ulf Andesson [editor.]
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 1468.Publisher: New York : Humana Press : Springer, ©2017Description: 1 online resource (xi, 252 pages) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9781493940356; 149394035X; 1493940333; 9781493940332Subject(s): RNA -- Laboratory manuals | RNA | RNA, Untranslated | RNA, Long Noncoding | Sequence Analysis, RNA | Enhancer Elements, Genetic | RNAGenre/Form: Laboratory Manual. | Electronic books. | Laboratory manuals. | Laboratory manuals. Additional physical formats: Print version:: Enhancer RNAs.DDC classification: 572.8/8 LOC classification: QP623Online resources: Click here to access online
Contents:
Cellular fractionation and isolation of chromatin-associated RNA / Thomas Conrad and Ulf Andersson Ørom -- Knockdown of nuclear-located enhancer RNAs and long ncRNAs using locked nucleic acid GapmeRs / Benoit T. Roux, Mark A. Lindsay, and James A. Heward -- Visualization of enhancer-derived noncoding RNA / Youtaro Shibayama, Stephanie Fanucchi, and Musa M. Mhlanga -- UV-RNA immunoprecipitation (UV-RIP) protocol in neurons / Katie Schaukowitch, Jae-Yeol Joo, and Tae-Kyung Kim -- Mapping long noncoding RNA chromatin occupancy using capture hybridization analysis of RNA targets (CHART) / Keith W. Vance -- Detecting long-range enhancer-promoter interactions by quantitative chromosome conformation capture / Wulan Deng and Gerd A. Blobel -- Deciphering noncoding RNA and chromatin interactions : multiplex chromatin interaction analysis by paired-end tag sequencing (mChIA-PET) / Jocelyn Choy and Melissa J. Fullwood -- Identification of transcribed enhancers by genome-wide chromatin imunoprecipitation sequencing / Steven Blinka [and others] -- Global run-on sequencing (GRO-Seq) / Alessandro Gardini -- Computational approaches for mining GRO-Seq data to identify and characterize active enhancers / Anusha Nagari [and others] -- Evaluating the stability of mRNAs and noncoding RNAs / Ana Carolina Ayupe and Eduardo M. Reis -- Novel method to quantify RNA-protein interactions in situ using FMTRIP and proximity ligation / C. Zurla [and others] -- In silico promoter recognition from deepCAGE data / Xinyi Yang and Annalisa Marsico -- Bioinformatics pipeline for transcriptome sequencing analysis / Sarah Djebali [and others] -- CRISPR/Cas9 genome editing in embryonic stem cells / Guillaume Andrey and Malte Spielmann -- Targeted gene activation using RNA-guided nucleases / Alexander Brown, Wendy S. Woods, and Pablo Perez-Pinera.
Summary: This volume provides a comprehensive overview of the experimental and computational methodologies used to study the function of long non-coding RNA (ncRNAs) expressed from enhancers. Chapter detail both wet-lab and dry-lab techniques and annotating long ncRNAs and exploring transcription by assessing where transcription starts and generally how it occurs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Enhancer RNAs: Methods and Protocols aims to ensure successful results in this rapidly developing field.
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Includes bibliographical references and index.

Cellular fractionation and isolation of chromatin-associated RNA / Thomas Conrad and Ulf Andersson Ørom -- Knockdown of nuclear-located enhancer RNAs and long ncRNAs using locked nucleic acid GapmeRs / Benoit T. Roux, Mark A. Lindsay, and James A. Heward -- Visualization of enhancer-derived noncoding RNA / Youtaro Shibayama, Stephanie Fanucchi, and Musa M. Mhlanga -- UV-RNA immunoprecipitation (UV-RIP) protocol in neurons / Katie Schaukowitch, Jae-Yeol Joo, and Tae-Kyung Kim -- Mapping long noncoding RNA chromatin occupancy using capture hybridization analysis of RNA targets (CHART) / Keith W. Vance -- Detecting long-range enhancer-promoter interactions by quantitative chromosome conformation capture / Wulan Deng and Gerd A. Blobel -- Deciphering noncoding RNA and chromatin interactions : multiplex chromatin interaction analysis by paired-end tag sequencing (mChIA-PET) / Jocelyn Choy and Melissa J. Fullwood -- Identification of transcribed enhancers by genome-wide chromatin imunoprecipitation sequencing / Steven Blinka [and others] -- Global run-on sequencing (GRO-Seq) / Alessandro Gardini -- Computational approaches for mining GRO-Seq data to identify and characterize active enhancers / Anusha Nagari [and others] -- Evaluating the stability of mRNAs and noncoding RNAs / Ana Carolina Ayupe and Eduardo M. Reis -- Novel method to quantify RNA-protein interactions in situ using FMTRIP and proximity ligation / C. Zurla [and others] -- In silico promoter recognition from deepCAGE data / Xinyi Yang and Annalisa Marsico -- Bioinformatics pipeline for transcriptome sequencing analysis / Sarah Djebali [and others] -- CRISPR/Cas9 genome editing in embryonic stem cells / Guillaume Andrey and Malte Spielmann -- Targeted gene activation using RNA-guided nucleases / Alexander Brown, Wendy S. Woods, and Pablo Perez-Pinera.

Online resource; title from PDF title page (SpringerProtocol, viewed October 5, 2016).

This volume provides a comprehensive overview of the experimental and computational methodologies used to study the function of long non-coding RNA (ncRNAs) expressed from enhancers. Chapter detail both wet-lab and dry-lab techniques and annotating long ncRNAs and exploring transcription by assessing where transcription starts and generally how it occurs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Enhancer RNAs: Methods and Protocols aims to ensure successful results in this rapidly developing field.

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