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Pipeline publication

[…] region was calculated relative to control sequences randomly selected from similar background. The top 20 motifs with the highest z-scores were performed the multiple sequence alignment using CLUSTALW. The output file was submitted to the WebLogo3 to generate the sequence logo. To investigate whether YB-1 binding sites are enriched on any pre-miRNAs, the iCLIP cDNA counts were normalized to the expression levels of individual mature miRNA detected by small RNA-seq analysis., The iCLIP cDNA counts for YB-1 crosslink sites could be viewed using IGV tool (www.broadinstitute.org/igv/) by uploading a tdf file from www.sibcb.ac.cn/hui.asp., The short reads of small RNA-seq data were processed by cutadapt () to trim the adaptor sequences, and aligned to human genome (hg19) by bowtie () using the parameter of ‘-v1 –best –strata –k11 –m10’. We used the BEDTools () and the GFF3 file downloaded from miRBase () to quantify the aligned reads on each miRNA. The expression values of miRNAs were normalized by the total number of aligned reads in each library., The human U251-MG and HEK 293T cells were grown in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum. Cells were transfected with control siRNA (5′- ATCCCGUACGCGGAAUACUdTdT-3′) and YB-1 siRNA (5′-GGUCAUCGCAACGAAGGUUdTdT-3′). Stable cell lines expressing control- or YB-1-specific shRNAs were established as previously described using lentivirus system ()., To clone pri-miRNA plasmids, PCR fragments containing pri-miR-24–1, pri-miR-29b-2, pri-miR-29b-1-29a, pri-miR-29 […]

Pipeline specifications

Software tools cutadapt, Bowtie, BEDTools