Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 10
Release date: Dec 5 2013
Last update date: Oct 24 2018
Access: Public
Chemicals: Nucleotides
Dataset link Differential Protein Occupancy Profiling of the mRNA Transcriptome

Experimental Protocol


We generated protein occupancy cDNA libraries for two biological replicates. Briefly, we crosslinked 4SU-labeled MCF7 cells and purified protein-mRNA complexes using oligo(dT)-beads. The precipitate was treated with RNAse I to reduce the protein-crosslinked RNA fragments to a length of about 30-60 nt. To remove non-crosslinked RNA, protein-RNA complexes were precipitated with ammonium sulfate and blotted onto nitrocellulose. The RNA was recovered by Proteinase K treatment, ligated to cloning adapters, and reverse transcribed. The resulting cDNA libraries were PCR-amplified and next-generation sequenced.

Repositories


GEO

GSE49831

ArrayExpress

E-GEOD-49831

ENA

SRP028887

BioProject

PRJNA215685

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Contact


Markus Landthaler

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