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Items: 1 to 20 of 438

1.

PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins.

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T.

J Vis Exp. 2010 Jul 2;(41). pii: 2034. doi: 10.3791/2034.

2.

PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins.

Spitzer J, Hafner M, Landthaler M, Ascano M, Farazi T, Wardle G, Nusbaum J, Khorshid M, Burger L, Zavolan M, Tuschl T.

Methods Enzymol. 2014;539:113-61. doi: 10.1016/B978-0-12-420120-0.00008-6.

3.

iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.

Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J.

J Vis Exp. 2011 Apr 30;(50). pii: 2638. doi: 10.3791/2638.

4.

PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites.

Danan C, Manickavel S, Hafner M.

Methods Mol Biol. 2016;1358:153-73. doi: 10.1007/978-1-4939-3067-8_10.

5.

Transcriptome-wide Identification of RNA-binding Protein Binding Sites Using Photoactivatable-Ribonucleoside-Enhanced Crosslinking Immunoprecipitation (PAR-CLIP).

Maatz H, Kolinski M, Hubner N, Landthaler M.

Curr Protoc Mol Biol. 2017 Apr 3;118:27.6.1-27.6.19. doi: 10.1002/cpmb.35.

PMID:
28369676
6.

PAR-CLIP and streamlined small RNA cDNA library preparation protocol for the identification of RNA binding protein target sites.

Benhalevy D, McFarland HL, Sarshad AA, Hafner M.

Methods. 2017 Apr 15;118-119:41-49. doi: 10.1016/j.ymeth.2016.11.009. Epub 2016 Nov 18.

PMID:
27871973
7.

Cross-linking and immunoprecipitation of nuclear RNA-binding proteins.

Li Q, Uemura Y, Kawahara Y.

Methods Mol Biol. 2015;1262:247-63. doi: 10.1007/978-1-4939-2253-6_15.

PMID:
25555586
8.

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T.

Cell. 2010 Apr 2;141(1):129-41. doi: 10.1016/j.cell.2010.03.009.

9.

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).

Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang MY, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW.

Nat Methods. 2016 Jun;13(6):508-14. doi: 10.1038/nmeth.3810. Epub 2016 Mar 28.

10.

Identification of RNA-protein interaction networks using PAR-CLIP.

Ascano M, Hafner M, Cekan P, Gerstberger S, Tuschl T.

Wiley Interdiscip Rev RNA. 2012 Mar-Apr;3(2):159-77. doi: 10.1002/wrna.1103. Epub 2011 Dec 27. Review.

11.

Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Experimental Procedures.

Han T, Kim JK.

Methods Mol Biol. 2016;1361:77-90. doi: 10.1007/978-1-4939-3079-1_5.

PMID:
26483017
12.

Genome-Wide Profiling of RNA-Protein Interactions Using CLIP-Seq.

Stork C, Zheng S.

Methods Mol Biol. 2016;1421:137-51. doi: 10.1007/978-1-4939-3591-8_12.

PMID:
26965263
13.

CLIPdb: a CLIP-seq database for protein-RNA interactions.

Yang YC, Di C, Hu B, Zhou M, Liu Y, Song N, Li Y, Umetsu J, Lu ZJ.

BMC Genomics. 2015 Feb 5;16:51. doi: 10.1186/s12864-015-1273-2.

14.

Transcriptome-wide identification of in vivo interactions between RNAs and RNA-binding proteins by RIP and PAR-CLIP assays.

González-Buendía E, Saldaña-Meyer R, Meier K, Recillas-Targa F.

Methods Mol Biol. 2015;1288:413-28. doi: 10.1007/978-1-4939-2474-5_24.

PMID:
25827894
15.

Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins.

Garzia A, Meyer C, Morozov P, Sajek M, Tuschl T.

Methods. 2017 Apr 15;118-119:24-40. doi: 10.1016/j.ymeth.2016.10.007. Epub 2016 Oct 17. Review.

PMID:
27765618
16.

In vivo and transcriptome-wide identification of RNA binding protein target sites.

Jungkamp AC, Stoeckius M, Mecenas D, Grün D, Mastrobuoni G, Kempa S, Rajewsky N.

Mol Cell. 2011 Dec 9;44(5):828-40. doi: 10.1016/j.molcel.2011.11.009.

17.

Mapping the Transcriptome-Wide Landscape of RBP Binding Sites Using gPAR-CLIP-seq: Bioinformatic Analysis.

Freeberg MA, Kim JK.

Methods Mol Biol. 2016;1361:91-104. doi: 10.1007/978-1-4939-3079-1_6.

PMID:
26483018
18.

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins.

Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M.

Nat Methods. 2011 May 15;8(7):559-64. doi: 10.1038/nmeth.1608.

PMID:
21572407
19.
20.

Insights into the design and interpretation of iCLIP experiments.

Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K, Ule J.

Genome Biol. 2017 Jan 16;18(1):7. doi: 10.1186/s13059-016-1130-x.

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