Dataset features

Specifications


Dataset type: Other
Number of samples: 7
Release date: Apr 21 2013
Last update date: Nov 27 2018
Access: Public
Diseases: Neoplasms
Chemicals: Azacitidine, Cytosine
Mutations: c|SUB|C||G
Dataset link Identification of direct targets and modified bases of RNA cytosine methyltransferases

Experimental Protocol


The general design of Aza-IP involves nine steps: 1) Expression of an epitope-tagged m5C-RMT derivative (or use of an antibody capable of immuno-precipitating the RNA-bound enzyme), 2) cell growth in the presence of 5-aza-C, which incorporates at low/moderate levels into nascent RNA, 3) cell lysis, 4) immuno-precipitation of the subject m5C-RMT, a portion of which is covalently attached to target RNAs bearing 5-aza-C, 5) stringent washing to remove RNA contaminants, 6) RNA fragmentation, release and purification, 7) ligation of adaptor oligos to the RNA, and the creation of a cDNA library in a manner that enables strand-specific assignments, 8) cDNA sequencing, and 9), mapping and examination of sequence reads to define RNA targets and site of cross-linking/catalysis.

Repositories


GEO

GSE38957

ArrayExpress

E-GEOD-38957

ENA

SRP013942

BioProject

PRJNA169525

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