Gene and transcript quantification files are annotated to GENCODE V24 (GRCh38), V19 (hg19), or M4 (mm10).Pipeline files are mapped to GRCh38, hg19, or mm10 sequences.
Replicates should match in terms of read length and run type. The sequencing platform used should be indicated. The experiments must pass routine metadata audits in order to be released. RBPs with non-typical binding patterns (including binding to rRNA, snRNAs, or other repetitive elements or multicopy sequences, broad binding to entire transcripts or transcript regions, or binding to specific RNA families) may pass via exemption. Narrow binding RBPs should have a FRiP score over enriched peaks of at least 0.005. The experiment passes if both rescue and self consistency ratios are less than 2. Replicate concordance is measured by calculating IDR values (Irreproducible Discovery Rate). eCLIP experiments should have 1 million unique fragments or have saturated peak detection in each biological replicate. Each eCLIP-seq experiment should have a corresponding size-matched input control experiment, with matching run type and read length. Please see the linked documents for transcription factor standards (May 2016), histone modification and chromatin-associated protein standards (October 2016), and RNA binding protein standards (November 2016). Antibodies must be characterized according to standards set by the ENCODE Consortium. Experiments should have two or more biological replicates, isogenic or anisogenic. PMID 21633356.Experimental guidelines for eCLIP experiments can be found here. "Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data". ^ Zhang, Chaolin Darnell, Robert B (1 June 2011). "iCLIP: protein-RNA interactions at nucleotide resolution". ^ Huppertz, Ina Attig, Jan D'Ambrogio, Andrea Easton, Laura E Sibley, Christopher R Sugimoto, Yoichiro Tajnik, Mojca König, Julian Ule, Jernej (February 2014). "Global protein-RNA interaction mapping at single nucleotide resolution by iCLIP-seq". ^ Yao, Chengguo Weng, Lingjie Shi, Yongsheng (20 February 2014). "Protein–RNA interactions: new genomic technologies and perspectives". CLIP is an antibody-based technique used to study RNA-protein interactions related to RNA immunoprecipitation (RIP), but differs from RIP in the use of. ^ König, Julian Zarnack, Kathi Luscombe, Nicholas M. This helps to identify PCR over-amplification effects in the high-throughput sequencing step and therefore improves the quantification of binding events. The primer used for reverse transcription can contain a random sequence, which can be used to barcode cDNAs. The small amount of resulting cDNAs is then PCR amplified and sequenced using a next-generation sequencing platform. Analogous resolution can be obtained with standard HITS-CLIP methods, using the observation that RT that does read through the cross link site has a high error rate, which can be used to deduce the position of the crosslink ("Crosslink induced mutation site" (CIMS) analysis ). The RNA is then reverse transcribed, causing cDNAs to often truncate at the crosslink site, which is the key insight and unique feature in the development of iCLIP, as it allows identification of the site of RNA-protein interaction at high resolution. The radiolabelled protein-RNA complexes are then excised from nitrocellulose, and treated with proteinase to release the RNA, leaving one or two amino acids at the crosslink site of the RNA. As with all CLIP methods, iCLIP allows for a very stringent purification of the linked protein-RNA complexes, using immunoprecipitation followed by SDS-PAGE and transfer to nitrocellulose. This cross-linking step has generally less background than RNA immunoprecipitation protocols. The method uses UV light to covalently bind proteins and RNA molecules. 
ICLIP (individual-nucleotide resolution Cross-Linking and ImmunoPrecipitation) is a method used for identifying protein-RNA interactions. Not to be confused with Intramembrane protease, sometimes abbreviated I-CLiP.
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