RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts

By Jack D. Keene, Jordan M. Komisarow, Matthew B. Friedersdorf. Nature Protocols, 2006

644 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b2bf4f110362d7d5de85b6302a35df12f2833d23

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Citations in the corpus

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data (2011, positive): “Two of the most established methods for the investigation of these interactions are RIP-Chip [2] or RIP-seq [3,4] and crosslinking and immunoprecipitation (CLIP) [5].”
Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. (2011, background): “Previously, RIP-chip (RBP ImmunoPrecipitation and microarray analysis) (Keene et al., 2006) has identified numerous functional mRNA targets of RBPs, including HuR (Lal et al., 2004; de Silanes et al., 2004; Mukherjee et al., 2009).”
Predicting RNA-Protein Interactions Using Only Sequence Information (2011, background): “Although large-scale experimental analyses of RPIs such as RNAcompete [23] , RIP-Chip [24] , HITS-CLIP [25] , PAR-CLIP [8] are now providing valuable data about networks of RNA-protein interactions, these experiments are expensive and time-consuming.”
Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs (2011, neutral): “RNA Immunoprecipitation and Analysis Cells were lysed on ice 48 hr after transfection with MS2 plasmids (Kim et al., 2009), and RIPs were performed as previously described (Keene et al., 2006).”
RBPmap: a web server for mapping binding sites of RNA-binding proteins (2014, methodology): “Among them are the Ribonucleoprotein immunoprecipitation (RIP) method (4) and the more advanced RIP-chip (5), as well as several cross-linking based methods such as CLIP (cross-linking immunoprecipitation) (6), CLIP-seq / HITS-CLIP (7), iCLIP (8) and PAR-CLIP (9).”
Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. (2008, methodology): “…identification of RNA targets for different trans-factors can also be achieved by some new approaches such as a cross-linking/immunoprecipitation (CLIP) (Ule et al. 2003), RNP immunoprecipitation (RIP) (Keene et al. 2006; Townley-Tilson et al. 2006), and genomic SELEX (Lorenz et al. 2006).”
Revealing protein–lncRNA interaction (2015, methodology): “RIP-Chip [55] and RIP-Seq [56] are high-throughput antibody-based techniques in which bound RNA is obtained through immunoprecipitation of its protein partner; then, the identification of the bound transcripts is performed via microarray (RIP-chip) or RNA-Seq (RIP-”
Integrative regulatory mapping indicates that the RNA-binding protein HuR (ELAVL1) couples pre-mRNA processing and mRNA stability (2011, methodology): “RIP-Chip Protocol was performed as described in Keene et al. (2006) with anti-FLAG M2-conjugated beads or mouse IgG-conjugated beads was used for immunoprecipitation reaction.”