title: GSM2258635: F1 control repB; Homo sapiens; RIP-Seq
library_construction_protocol: The cells are rinsed with PBS and crosslinked with 0.15mJ/cm2 UV-C light. After crosslinking, the cells are pelleted by centrifugation, snap-frozen in liquid nitrogen and kept at -80˚C until use. Cells are lysed with 0.5mL of lysis buffer, mildly sonicated and immunoprecipitated with anti-FLAG beads for 1hr at ˚C. The beads are washed with lysis buffer and bound material is eluted with 3xFLAG peptide (250µg/mL). The eluate is then incubated with MyONEC1 beads to collect biotinylated target protein, after which the beads are washed with high-stringency buffers (0.1%SDS, 1M NaCl, 0.5% LiDS, 0.5M LiCl and 1% SDS, 0.5M LiCl) to aggressively remove non-specific interactors. 3’-linkers are then ligated with T4 RNA Ligase 1, excess adapters are washed away and 3’-tagged, cross-linked RNA is released with proteinase K digestion and column purification (Zymo DNA Clean & Concentrator). Reverse transcription is carried out with SuperScript III and barcoded reverse-transcription primers. After reverse transcription, relevant samples are mixed and the cDNA is separated on a 6% 6M Urea PAA gel. Size fractionated cDNA is then processed essentially as described in the iCLIP protocol to generate sequencing libraries (König, J. et al. iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J. Vis. Exp. (2011). doi:10.3791/2638). uvCLAP reads contain two custom barcodes adjacent to the 5'- and 3'-adapters. The 5 nt 5'-barcodes are flanked by 5 random nt according to the pattern NNNTTTTTNN (N: random nucleotide, T: barcode nucletide) and specify the pulldown condition. The 5 nt semi-random 3'-barcodes DRYYR and DYRRY (D: not C, R: purine, Y: pyrimidine) are used to distinguish the two replicates of each experiment. The 5'-barcodes are located at the first 10 nucleotides of the first mate reads. The read pairs align forward/reverse, thus the reverse complement of the 3'-barcodes is located at the first 5 nucleotides of the second mate reads.
attributes.tag: GEO Accession
attributes.value: GSM2258635