GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE49831 Query DataSets for GSE49831
Status Public on Dec 05, 2013
Title Differential Protein Occupancy Profiling of the mRNA Transcriptome
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We have developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing (Baltz and Munschauer et al. 2012). Our current work focuses on streamlining and extending protein occupancy profiling on poly(A)-RNA. Our objectives are to identify previously unknown protein-bound transcripts and, more importantly, to assess global and local differences in protein occupancy across different biological conditions. To this end, we have implemented poppi, the first pipeline for differential analysis of protein occupancy profiles. We have applied our analysis pipeline to pinpoint changes in occupancy profiles of MCF7 cells against already published HEK293 cells [GSE38157].
Overall design 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.
Contributor(s) Landthaler M
Citation(s) 24417896
Submission date Aug 13, 2013
Last update date May 15, 2019
Contact name Markus Landthaler
Phone +49-30-9406-3026
Organization name Max-Delbrück-Center for Molecular Medicine
Department Berlin Institute for Medical Systems Biology
Street address Robert-Rössle-Straße 10
City Berlin
ZIP/Postal code 13125
Country Germany
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (10)
GSM1207878 MCF7 profiling library 1
GSM1207879 MCF7 profiling library 2
GSM1269464 HEK293 4suRNA
BioProject PRJNA215685
SRA SRP028887

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE49831_HEK293_halflives.txt.gz 164.4 Kb (ftp)(http) TXT
GSE49831_MCF7_ProtOccProf_4SU_consensus_TC_minus.bedGraph.gz 6.0 Mb (ftp)(http) BEDGRAPH
GSE49831_MCF7_ProtOccProf_4SU_consensus_TC_plus.bedGraph.gz 6.2 Mb (ftp)(http) BEDGRAPH
GSE49831_MCF7_ProtOccProf_4SU_consensus_coverage_minus.bedGraph.gz 111.6 Mb (ftp)(http) BEDGRAPH
GSE49831_MCF7_ProtOccProf_4SU_consensus_coverage_plus.bedGraph.gz 116.6 Mb (ftp)(http) BEDGRAPH
GSE49831_MCF7_halflives.txt.gz 159.8 Kb (ftp)(http) TXT
GSE49831_RAW.tar 520.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap