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Series GSE50989 Query DataSets for GSE50989
Status Public on Nov 07, 2013
Title Advancing Functional Utility of PAR-CLIP by Quantifying Background Binding to mRNAs and lncRNAs
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Non-coding RNA profiling by high throughput sequencing
Summary We developed a method for measuring non-specific background in PAR-CLIP data demonstrating that covalently crosslinked background binding is common, reproducible and apparently universal. Furthermore, we show that quantitative determination of background is essential for identifying targets of weakly binding RNA-binding proteins and can substantially improve motif analysis.
 
Overall design To define background binding events in PAR-CLIP data we performed the standard PAR-CLIP protocol (Hafner et al., Cell 2010.) on lysates expressing a commonly used non-RBP control, FLAG-GFP. After FLAG-tag immunopurification of UV 365nm irradiated lysates prepared from cells supplemented with 4-thiouridine (4SU), RNA was partially digested with RNase T1, radiolabeled and separated by SDS-PAGE. Reads were sequenced by Illumina HiSeq. PAR-CLIP was also performed for HuR. Included as well is a total from lysates treated like PAR-CLIP, but without immunoprecipitation (see sample description for more detail).
 
Contributor(s) Friedersdorf MB, Keene JD
Citation(s) 24393468
Submission date Sep 18, 2013
Last update date May 15, 2019
Contact name Matthew Burk Friedersdorf
E-mail(s) mbf2@duke.edu
Phone (919)684-5589
Organization name Duke University
Department Molecular Genetics & Microbiology
Lab Keene
Street address 207 Research Drive
City Durham
State/province NC
ZIP/Postal code 27705
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (6)
GSM1234280 PAR-CLIP background, ~20KDa; G20
GSM1234281 PAR-CLIP background, ~35KDa; G35
GSM1234282 PAR-CLIP background, ~45KDa; G45
Relations
BioProject PRJNA219483
SRA SRP030015

Download family Format
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Supplementary file Size Download File type/resource
GSE50989_RAW.tar 288.1 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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