SPELL - Nematode

Citation	Jovanovic M, Reiter L, Clark A, Weiss M, Picotti P, Rehrauer H, Frei A, Neukomm L, Kaufman E, Wollscheid B, Simard MJ, Miska E, Aebersold R, Gerber AP, Hengartner MO. RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. Genome Res, 2012.
PubMed ID	22454234
Short Description	RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. GEO Record: GSE32941 GSE32943 GSE32944 Platform: GPL14724 Download gene-centric, log2 transformed data: WBPaper00040925.ce.mr.csv
# of Conditions	6
Full Description	MicroRNAs (miRNAs) are small, noncoding RNAs that negatively regulate gene expression. As miRNAs are involved in a wide range of biological processes and diseases, much effort has been invested in identifying their mRNA targets. Here, we present a novel combinatorial approach, RIP-chip-SRM (RNA-binding protein immunopurification + microarray + targeted protein quantification via selected reaction monitoring), to identify de novo high-confidence miRNA targets in the nematode Caenorhabditis elegans. We used differential RIP-chip analysis of miRNA-induced silencing complexes from wild-type and miRNA mutant animals, followed by quantitative targeted proteomics via selected reaction monitoring to identify and validate mRNA targets of the C. elegans bantam homolog miR-58. Comparison of total mRNA and protein abundance changes in mir-58 mutant and wild-type animals indicated that the direct bantam/miR-58 targets identified here are mainly regulated at the level of protein abundance, not mRNA stability. Experimental Details: WBPaper00040925:WS5041_Rep1 WBPaper00040925:WS4303_Rep1 WBPaper00040925:WS5041_Rep2 WBPaper00040925:WS4303_Rep2 WBPaper00040925:WS5041_Rep3 WBPaper00040925:WS4303_Rep3.
Tags	Method: microarray, Species: Caenorhabditis elegans, Topic: gene silencing by miRNA