FASTQ files for two biological replicates in each condition were trimmed as described above. The reads were aligned to the human genome build hg19 by gsnap aligner v.2017-04-21 with two mismatches allowed (34). The RIP-seq analysis was performed with RIPSeeker R package v.1.18.0 (35) with the parameters as follows: uniqueHit = TRUE, assignMultihits = TRUE, rerunWithDisambiguatedMultihits = TRUE, and automatic bin size selection. Ensembl BioMart build 75 was used for functional annotation of the RIP-seq results. RNA species significantly enriched (adjusted P value threshold < 0.05) above the siE2F1 control RIP are recorded in table S4. RIP sequencing data have been deposited in NCBI’s GEO and are accessible through GEO Series accession number GSE111961.

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.