Computational protocol: Effective heritable gene knockdown in zebrafish using synthetic microRNAs

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Protocol publication

[…] To select target sequences, we mainly used the BLOCK-IT RNAi Designer website from Invitrogen that is optimized for artificial miRNA-mediated knockdown (http://rnaidesigner.lifetechnologies.com/rnaiexpress/setOption.do?designOption=mirna&pid=8945441149181672314). Among other tools and websites, we used also GenScript's siRNA Design Center (www.genscript.com/design_center.html), siSearch (sidirect2.rnai.jp/), IDT SciTools RNAi Design (http://sg.idtdna.com/Scitools/Applications/RNAi/RNAi.aspx/), Target Finder supplied by Ambion (http://www.ambion.com/techlib/misc/siRNA_finder.html), Dharmacom RNAi design centre (http://dharmacon.gelifesciences.com/design-center/) and siSPOTR tools (https://sispotr.icts.uiowa.edu/).Targetscan Fish (http://www.targetscan.org/fish_62/) is also useful to obtain complete and accurate 3′-UTR sequences of a gene of interest in zebrafish. […]

Pipeline specifications