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PMID: 18158127 Published · ppublish English Journal Article Review

Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing.

Methods (San Diego, Calif.) ·Vol. 44 ·No. 1 ·2008-01-00 ·Pages 3-12

Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, Holoch D, Lim C, Tuschl T

Abstract

Distinct classes of small RNAs, 20-32 nucleotides long, play important regulatory roles for diverse cellular processes. It is therefore important to identify and quantify small RNAs as a function of development, tissue and cell type, in normal and disease states. Here we describe methods to prepare cDNA libraries from pools of small RNAs isolated from organisms, tissues or cells. These methods enable the identification of new members or new classes of small RNAs, and they are also suitable to obtain miRNA expression profiles based on clone count frequencies. This protocol includes the use of new deep sequencing methods (454/Roche and Solexa) to facilitate the characterization of diverse sequence pools of small RNAs.

MeSH Terms
Animals Gene Library Humans MicroRNAs/genetics,isolation & purification Oligonucleotide Array Sequence Analysis/methods Regulatory Sequences, Ribonucleic Acid/genetics
Chemicals
MicroRNAs Regulatory Sequences, Ribonucleic Acid
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Hafner Markus
Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA.
Landgraf Pablo
Ludwig Janos
Rice Amanda
Ojo Tolulope
Lin Carolina
Holoch Daniel
Lim Cindy
Tuschl Thomas
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Article Info
Journal
Methods (San Diego, Calif.)
Abbr.
Methods
ISSN
1046-2023
DOI
10.1016/j.ymeth.2007.09.009
Published
2008-01-00
Pages
3-12
Language
English
Region
United States
NLM ID
9426302
PMCID
PMC2847350
Subset
IM
Grants
NIGMS NIH HHS · P01 GM073047-040001 · United States
NIGMS NIH HHS · P01 GM073047-01 · United States
NIGMS NIH HHS · P01 GM073047-010001 · United States
NIGMS NIH HHS · P01 GM073047-019001 · United States
NIGMS NIH HHS · P01 GM073047-04 · United States
NIGMS NIH HHS · P01 GM073047-050001 · United States
Howard Hughes Medical Institute · United States
NIGMS NIH HHS · P01 GM073047-05 · United States
NIGMS NIH HHS · P01 GM073047-02 · United States
NIGMS NIH HHS · P01 GM073047-020001 · United States
NIGMS NIH HHS · P01 GM073047-030001 · United States
NIGMS NIH HHS · P01 GM073047-03 · United States
NIGMS NIH HHS · P01 GM073047 · United States
External Links
PubMed source DOI: 10.1016/j.ymeth.2007.09.009 PMC Full Text View journal details
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