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Items: 1 to 20 of 84

1.

Metabolic labeling of newly transcribed RNA for high resolution gene expression profiling of RNA synthesis, processing and decay in cell culture.

Rädle B, Rutkowski AJ, Ruzsics Z, Friedel CC, Koszinowski UH, Dölken L.

J Vis Exp. 2013 Aug 8;(78). doi: 10.3791/50195.

2.
4.

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.

Windhager L, Bonfert T, Burger K, Ruzsics Z, Krebs S, Kaufmann S, Malterer G, L'Hernault A, Schilhabel M, Schreiber S, Rosenstiel P, Zimmer R, Eick D, Friedel CC, Dölken L.

Genome Res. 2012 Oct;22(10):2031-42. doi: 10.1101/gr.131847.111. Epub 2012 Apr 26.

5.

Enriching s4 U-RNA Using Methane Thiosulfonate (MTS) Chemistry.

Duffy EE, Simon MD.

Curr Protoc Chem Biol. 2016 Dec 7;8(4):234-250. doi: 10.1002/cpch.12.

PMID:
27925666
6.

Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection.

Marcinowski L, Lidschreiber M, Windhager L, Rieder M, Bosse JB, Rädle B, Bonfert T, Györy I, de Graaf M, Prazeres da Costa O, Rosenstiel P, Friedel CC, Zimmer R, Ruzsics Z, Dölken L.

PLoS Pathog. 2012 Sep;8(9):e1002908. doi: 10.1371/journal.ppat.1002908. Epub 2012 Sep 6.

7.

Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification.

Schwarzl T, Higgins DG, Kolch W, Duffy DJ.

J Mol Biol. 2015 Oct 23;427(21):3368-74. doi: 10.1016/j.jmb.2015.09.006. Epub 2015 Sep 9.

PMID:
26362006
8.

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay.

Dölken L, Ruzsics Z, Rädle B, Friedel CC, Zimmer R, Mages J, Hoffmann R, Dickinson P, Forster T, Ghazal P, Koszinowski UH.

RNA. 2008 Sep;14(9):1959-72. doi: 10.1261/rna.1136108. Epub 2008 Jul 24.

9.

Simultaneous measurement of genome-wide transcription elongation speeds and rates of RNA polymerase II transition into active elongation with 4sUDRB-seq.

Fuchs G, Voichek Y, Rabani M, Benjamin S, Gilad S, Amit I, Oren M.

Nat Protoc. 2015 Apr;10(4):605-18. doi: 10.1038/nprot.2015.035. Epub 2015 Mar 26.

PMID:
25811895
10.

4-Thiouridine Labeling to Analyze mRNA Turnover in Schizosaccharomyces pombe.

Mata J, Wise JA.

Cold Spring Harb Protoc. 2017 May 1;2017(5):pdb.prot091645. doi: 10.1101/pdb.prot091645.

PMID:
28461655
11.

Metabolic tagging and purification of nascent RNA: implications for transcriptomics.

Friedel CC, Dölken L.

Mol Biosyst. 2009 Nov;5(11):1271-8. doi: 10.1039/b911233b. Epub 2009 Aug 26. Review.

PMID:
19823741
13.

Synthesis of biotin-labeled RNA for gene expression measurements using oligonucleotide arrays.

Vázquez AE, Nie L, Yamoah EN.

Methods Mol Biol. 2009;493:21-9. doi: 10.1007/978-1-59745-523-7_2.

14.

Dynamic regulation of mRNA decay during neural development.

Burow DA, Umeh-Garcia MC, True MB, Bakhaj CD, Ardell DH, Cleary MD.

Neural Dev. 2015 Apr 21;10:11. doi: 10.1186/s13064-015-0038-6.

15.

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry.

Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD.

Mol Cell. 2015 Sep 3;59(5):858-66. doi: 10.1016/j.molcel.2015.07.023.

16.

Site-specific 4-thiouridine incorporation into RNA molecules.

Yu YT.

Methods Enzymol. 2000;318:71-88. No abstract available.

PMID:
10889981
17.

Transcriptomics: advances and approaches.

Dong Z, Chen Y.

Sci China Life Sci. 2013 Oct;56(10):960-7. doi: 10.1007/s11427-013-4557-2. Epub 2013 Oct 5. Review.

PMID:
24091688
18.

A Nonradioactive Assay to Measure Production and Processing of Ribosomal RNA by 4sU-Tagging.

Burger K, Eick D.

Methods Mol Biol. 2016;1455:121-31. doi: 10.1007/978-1-4939-3792-9_10.

PMID:
27576715
19.

Metabolic labeling and recovery of nascent RNA to accurately quantify mRNA stability.

Russo J, Heck AM, Wilusz J, Wilusz CJ.

Methods. 2017 May 1;120:39-48. doi: 10.1016/j.ymeth.2017.02.003. Epub 2017 Feb 20.

PMID:
28219744
20.

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast.

Miller C, Schwalb B, Maier K, Schulz D, Dümcke S, Zacher B, Mayer A, Sydow J, Marcinowski L, Dölken L, Martin DE, Tresch A, Cramer P.

Mol Syst Biol. 2011 Jan 4;7:458. doi: 10.1038/msb.2010.112.

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