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Series GSE86035 Query DataSets for GSE86035
Status Public on Oct 06, 2016
Title SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.
Organism Homo sapiens
Experiment type Other
Summary RNA metabolism is controlled by an expanding yet incomplete catalog of RNA binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull-down of twelve nuclear and cytoplasmic RBPs followed by quantitative mass-spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1923 human, 489 fly and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins.
Overall design eCLIP-seq was performed in biological replicate for AIFM1, NUMA1, RANGAP1, RNF219, VIM, ZNF184. Each sample has a size-matched input control for analysis
Contributor(s) Brannan KW, Jin W, Banks CA, Gilmore JM, Florens L, Washburn MP, Van Nostrand EL, Pratt GA, Schwinn MK, Daniels DL, Yeo GW
Citation(s) 27720645
Submission date Aug 25, 2016
Last update date May 15, 2019
Contact name Gene Yeo
Organization name UCSD
Street address 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (17)
GSM2291979 AIFM_eCLIP_Replicate1
GSM2291980 AIFM_eCLIP_Replicate2
GSM2291981 RNF219_Input
BioProject PRJNA340076
SRA SRP082930

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Supplementary file Size Download File type/resource
GSE86035_RAW.tar 515.6 Mb (http)(custom) TAR (of BB, BED, BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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