Transcriptomics

Dataset Information

297

Analysis of conditions leading to 3'UTR ribosome protected footprints


ABSTRACT: Ribosome profiling data from U2OS, HeLa and Kc167 cells under various lysis conditions and using immunoprecipitation to purifiy ribosome associated footprints. Two human cell lines (U2OS and HeLa cells) and a Drosophila melanogaster cell line (Kc167) are used to see if the 3'UTR reads are identified in each cell type. Immunoprecipitation of ribosomes is used to analyse if 3'UTR reads derive from ribosomes (are found with ribosome immunoprecipitates) and to which extent the lysis conditions contribute to the identification of the 3'UTR reads.

INSTRUMENT(S): Illumina HiSeq 2500

SUBMITTER: Mikael Bjorklund  

PROVIDER: E-MTAB-3135 | ArrayExpress | 2015-01-08

SECONDARY ACCESSION(S): ERP008887

REPOSITORIES: ArrayExpress, ENA

altmetric image

Publications

Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3' untranslated regions.

Miettinen Teemu P TP   Björklund Mikael M  

Nucleic acids research 20141229 2


Ribosome profiling identifies ribosome positions on translated mRNAs. A prominent feature of published datasets is the near complete absence of ribosomes in 3' untranslated regions (3'UTR) although substantial ribosome density can be observed on non-coding RNAs. Here we perform ribosome profiling in cultured Drosophila and human cells and show that different features of translation are revealed depending on the nuclease and the digestion conditions used. Most importantly, we observe high abundan  ...[more]

Similar Datasets

2015-01-08 | E-MTAB-2421 | ArrayExpress
2018-06-30 | E-MTAB-6938 | ArrayExpress
2014-07-31 | E-GEOD-59599 | ArrayExpress
2006-06-01 | E-MEXP-460 | ArrayExpress
| GSE69414 | GEO
| phs001825 | dbGaP
2015-10-16 | E-MTAB-2934 | ArrayExpress
2017-07-06 | E-MTAB-3189 | ArrayExpress
2015-03-09 | E-MTAB-2278 | ArrayExpress
2016-11-07 | E-MTAB-3815 | ArrayExpress