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Items: 1 to 50 of 143

1.

Kaposi's Sarcoma-Associated Herpesvirus Utilizes and Manipulates RNA N6-Adenosine Methylation To Promote Lytic Replication.

Ye F, Chen ER, Nilsen TW.

J Virol. 2017 Jul 27;91(16). pii: e00466-17. doi: 10.1128/JVI.00466-17. Print 2017 Aug 15.

2.

NOTE FROM THE EDITOR.

Nilsen TW.

RNA. 2016 May;22(5):viii. No abstract available.

3.

Erratum: Preparation of Nuclear Extracts from HeLa Cells.

Nilsen TW.

Cold Spring Harb Protoc. 2016 Jul 1;2016(7). doi: 10.1101/pdb.err094813. No abstract available.

PMID:
27371590
4.

Cotranslational microRNA mediated messenger RNA destabilization.

Tat TT, Maroney PA, Chamnongpol S, Coller J, Nilsen TW.

Elife. 2016 Apr 8;5. pii: e12880. doi: 10.7554/eLife.12880.

5.

Preparing Cellular DNA from Nuclei or Whole Cells.

Nilsen TW.

Cold Spring Harb Protoc. 2015 Sep 1;2015(9):pdb.prot086314. doi: 10.1101/pdb.prot086314.

PMID:
26330625
6.

Removal of rRNA from Deproteinized, Phenol-Extracted Total RNA by Hybrid Selection.

Nilsen TW.

Cold Spring Harb Protoc. 2015 Aug 3;2015(8):784-5. doi: 10.1101/pdb.prot086132.

PMID:
26240407
7.

Boundary Analysis to Determine the Minimal RNA Sequence Required for Protein Binding.

Nilsen TW.

Cold Spring Harb Protoc. 2015 Jul 1;2015(7):662-5. doi: 10.1101/pdb.prot081042.

PMID:
26134905
8.

Nucleotide analog interference mapping.

Nilsen TW.

Cold Spring Harb Protoc. 2015 Jun 1;2015(6):604-8. doi: 10.1101/pdb.prot081067.

PMID:
26034303
9.

Chemical modification interference.

Nilsen TW.

Cold Spring Harb Protoc. 2015 Jun 1;2015(6):599-603. doi: 10.1101/pdb.prot081059.

PMID:
26034302
10.

Measuring the length of poly(A) tails.

Nilsen TW.

Cold Spring Harb Protoc. 2015 Apr 1;2015(4):413-8. doi: 10.1101/pdb.prot081034.

PMID:
25834263
11.

Twenty years of RNA: then and now.

Nilsen TW.

RNA. 2015 Apr;21(4):471-3. doi: 10.1261/rna.051284.115. No abstract available.

12.

An alternative method for processing northern blots after capillary transfer.

Nilsen TW.

Cold Spring Harb Protoc. 2015 Mar 2;2015(3):314-8. doi: 10.1101/pdb.prot081026.

PMID:
25734064
13.

An intimate view of a spliceosome component.

Nilsen TW.

Elife. 2015 Feb 13;4:e06200. doi: 10.7554/eLife.06200.

14.

Poisoned primer extension.

Nilsen TW.

Cold Spring Harb Protoc. 2015 Jan 5;2015(1):pdb.prot080986. doi: 10.1101/pdb.prot080986.

PMID:
25561619
15.

Direct chemical sequencing of end-labeled RNA.

Nilsen TW.

Cold Spring Harb Protoc. 2015 Jan 5;2015(1):pdb.prot080937. doi: 10.1101/pdb.prot080937.

PMID:
25561618
16.

Mapping RNA-protein interactions using iodine footprinting.

Nilsen TW.

Cold Spring Harb Protoc. 2014 Dec 1;2014(12):1337-41. doi: 10.1101/pdb.prot080960.

PMID:
25447283
17.

Mapping RNA-protein interactions using hydroxyl-radical footprinting.

Nilsen TW.

Cold Spring Harb Protoc. 2014 Dec 1;2014(12):1333-6. doi: 10.1101/pdb.prot080952.

PMID:
25447282
18.

Preparation of cross-linked cellular extracts with formaldehyde.

Nilsen TW.

Cold Spring Harb Protoc. 2014 Sep 2;2014(9):1001-3. doi: 10.1101/pdb.prot080879.

PMID:
25183820
19.

Detecting RNA-RNA interactions using psoralen derivatives.

Nilsen TW.

Cold Spring Harb Protoc. 2014 Sep 2;2014(9):996-1000. doi: 10.1101/pdb.prot080861.

PMID:
25183819
20.

Detection of RNAs by 3'-end labeling and RNase H digestion.

Nilsen TW.

Cold Spring Harb Protoc. 2014 Jul 1;2014(7):789-92. doi: 10.1101/pdb.prot080796.

PMID:
24987142
21.

Reverse footprinting to map sites of RNA-protein interactions.

Nilsen TW.

Cold Spring Harb Protoc. 2014 Jun 2;2014(6):683-6. doi: 10.1101/pdb.prot080804.

PMID:
24890211
22.

RNase footprinting to map sites of RNA-protein interactions.

Nilsen TW.

Cold Spring Harb Protoc. 2014 Jun 2;2014(6):677-82. doi: 10.1101/pdb.prot080788.

PMID:
24890210
23.

3'-end labeling of RNA with [5'-32P]Cytidine 3',5'-bis(phosphate) and T4 RNA ligase 1.

Nilsen TW.

Cold Spring Harb Protoc. 2014 Apr 1;2014(4):444-6. doi: 10.1101/pdb.prot080713.

PMID:
24692494
24.

Molecular biology. Internal mRNA methylation finally finds functions.

Nilsen TW.

Science. 2014 Mar 14;343(6176):1207-8. doi: 10.1126/science.1249340. No abstract available.

PMID:
24626918
25.

Preparing size markers for gel electrophoresis.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Dec 1;2013(12):1186-9. doi: 10.1101/pdb.prot079426.

PMID:
24298031
26.

RNA sequencing by primer extension.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Dec 1;2013(12):1182-5. doi: 10.1101/pdb.prot079400.

PMID:
24298029
27.

High-yield synthesis of RNA using T7 RNA polymerase and plasmid DNA or oligonucleotide templates.

Nilsen TW, Rio DC, Ares M Jr.

Cold Spring Harb Protoc. 2013 Nov 1;2013(11). pii: pdb.prot078535. doi: 10.1101/pdb.prot078535.

PMID:
24184762
28.

Toeprinting.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Sep 1;2013(9):896-9. doi: 10.1101/pdb.prot077180.

PMID:
24003204
29.

The fundamentals of RNA purification.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Jul 1;2013(7):618-24. doi: 10.1101/pdb.top075838.

PMID:
23818674
30.
31.

Analysis of pre-mRNA splicing using HeLa cell nuclear extracts.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Jun 1;2013(6):584-7. doi: 10.1101/pdb.prot075184.

PMID:
23734029
32.

Preparation of Nuclear Extracts from HeLa cells.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Jun 1;2013(6):579-83. doi: 10.1101/pdb.prot075176. Erratum in: Cold Spring Harb Protoc. 2016;2016(7):pdb.err094813.

PMID:
23734028
33.

RNA structure determination using nuclease digestion.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Apr 1;2013(4):379-82. doi: 10.1101/pdb.prot072330.

PMID:
23547152
34.

Detecting RNA-protein interactions by photocross-linking using RNA molecules containing uridine analogs.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Mar 1;2013(3). pii: pdb.prot073569. doi: 10.1101/pdb.prot073569.

PMID:
23457347
35.

Site-specific labeling of RNA.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Mar 1;2013(3). pii: pdb.prot072918. doi: 10.1101/pdb.prot072918.

PMID:
23457342
36.

Gel purification of RNA.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Feb 1;2013(2):180-3. doi: 10.1101/pdb.prot072942.

PMID:
23378657
37.

RNA-friendly plasmid preparation.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Feb 1;2013(2):174-9. doi: 10.1101/pdb.prot072926.

PMID:
23378655
38.

Determining the yield of RNA synthesized in vitro.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Jan 1;2013(1). pii: pdb.prot072629. doi: 10.1101/pdb.prot072629.

PMID:
23282637
39.

Splinted ligation method to detect small RNAs.

Nilsen TW.

Cold Spring Harb Protoc. 2013 Jan 1;2013(1). pii: pdb.prot072611. doi: 10.1101/pdb.prot072611.

PMID:
23282636
40.

Selective precipitation of large RNAs.

Nilsen TW.

Cold Spring Harb Protoc. 2012 Dec 1;2012(12). pii: pdb.prot072322. doi: 10.1101/pdb.prot072322.

PMID:
23209142
41.

Removing rRNA from deproteinized, phenol-extracted total RNA by enzymatic digestion.

Nilsen TW.

Cold Spring Harb Protoc. 2012 Nov 1;2012(11):1187-8. doi: 10.1101/pdb.prot072124.

PMID:
23118366
42.

In vitro transcription of labeled RNA: synthesis, capping, and substitution.

Nilsen TW, Rio DC.

Cold Spring Harb Protoc. 2012 Nov 1;2012(11):1181-6. doi: 10.1101/pdb.prot072066.

PMID:
23118360
43.

A rapid, quantitative assay for direct detection of microRNAs and other small RNAs using splinted ligation.

Chamnongpol S, Maroney PA, Nilsen TW.

Methods Mol Biol. 2010;667:3-17. doi: 10.1007/978-1-60761-811-9_1.

PMID:
20827523
44.

Enrichment of poly(A)+ mRNA using immobilized oligo(dT).

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jul 1;2010(7):pdb.prot5454. doi: 10.1101/pdb.prot5454.

PMID:
20647358
45.

Guidelines for the use of RNA purification kits.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jul 1;2010(7):pdb.ip79. doi: 10.1101/pdb.ip79.

PMID:
20647349
46.

Determining the yield and quality of purified RNA.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.top82. doi: 10.1101/pdb.top82.

PMID:
20516190
47.

Nondenaturing agarose gel electrophoresis of RNA.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5445. doi: 10.1101/pdb.prot5445.

PMID:
20516183
48.

Polyacrylamide gel electrophoresis of RNA.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5444. doi: 10.1101/pdb.prot5444.

PMID:
20516182
49.

Removal of DNA from RNA.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5443. doi: 10.1101/pdb.prot5443.

PMID:
20516181
50.

Removal of ribosomal subunits (and rRNA) from cytoplasmic extracts before solubilization with SDS and deproteinization.

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5442. doi: 10.1101/pdb.prot5442.

PMID:
20516180

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