Project description:Purpose:We used eCLIP experiment to analyze binding profile of SERBP1 and its relationship with G4. Result: we found 505 high-confidence SERBP1 binding sites in Hela cells, and the analysis of sequence revealed transcriptome-wide enrichment of PQS in SERBP1-binding regions
Project description:U1A iCLIP-seq (individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled with RNA sequencing) analysis in HeLa cells
Project description:We hypothesized that RBM4 regulates HERVs by directly binding to their transcripts. To test this possibility, we performed photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP). We performed four independent PAR-CLIP replicates of our own using HAP1 cells stably expressing a FLAG-tagged RBM4 (FLAG-RBM4) transgene under control of a doxycycline-inducible promoter. Following metabolic labeling with 4-thiouridine (4SU) and crosslinking with ultraviolet light (UV) of 312 nm wavelength, we isolated RNA covalently linked to FLAG-RBM4. The RNA recovered from four biological replicates was converted into cDNA libraries and deep sequenced.
Project description:To identify the substrates of METTL5, we used crosslinking-assisted immunoprecipitation of overexpressed, FLAG-METTL5 followed by high throughput sequencing.
Project description:seCLIP-Seq (single-end enhanced crosslinking and immunoprecipitation) of STAT3, OCT4, and SRSF1 in TE03 (I3) human embryonic stem cells (hESCs)
Project description:Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was used to generate a transcriptome-wide binding map of hnRNP L. Supplementary file GSE37560_hnRNPL_crosslink_site.bed includes filtered crosslink sites of hnRNPL: combining data from all 3 experiments. 3 biological replicates of hnRNP L-specific and control (Flag) co-immunoprecipitated RNA after UV-crosslinking in HeLa cells
Project description:eCLIP was performed for ENO1 in HeLa cells, following the protocol described by Van Nostrand et al. (2016). Libraries for six immunoprecipitation and size-matched input controls were produced. In addition, libraries were produced for two no-crosslinking controls. The libraries were sequenced using paired-end sequencing (PE125) on an Illumina HiSeq2000 platform.