For the design of effective siRNA HIF‐1α target sequences, a siRNA design tool was applied siRNA design tool (eurofins, USA) and siRNA target sequences were obtained according to published criteria.14 , 15 For synthesis of siRNA HIF‐1α via in vitro transcription, the Silencer™ siRNA Construction Kit (Ambion, Austin, TX, USA) was used with modifications.16 Chemically synthesized GFP siRNA HIF‐1α was bought from Ambion (Ambion). For transient infection, cells were cultured and grown to 70%‐90% confluence, and then transfected with siRNAs using Lipofectamine 3000 (Invitrogen, Grand Island, NY, USA) according to the manufacturer’s procedure. After 48 hours, cells were used for migration assay or expression analysis. The siRNA sequences were as listed in Table 1 .
Sirna design tool
Manufactured by Eurofins
Sourced in United States
The SiRNA design tool is a software application that assists in the design of small interfering RNA (siRNA) sequences. It provides a platform for users to input their target genes or sequences, and the tool generates potential siRNA candidates that can be used for gene silencing experiments. The core function of this tool is to analyze input data and algorithmically generate siRNA sequences that meet specific design criteria, such as thermodynamic stability, specificity, and minimized off-target effects.
Automatically generated - may contain errors
Lab products found in correlation
4 protocols using sirna design tool
1
siRNA Knockdown of HIF-1α in Cells
2
Knockdown of endogenous COQ7 transcripts
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Knock down of endogenous COQ7 transcripts was performed using a pool of siRNA against- 5′-UTR: 5′-AGCAACCACUUCGUUGAACUU-3′ and 5′-ACUUCGUUGAACGGAACUGUU-3′; and 3′-UTR: 5′-ACCUGUUUCUCUGCAAAUGUU-3′. siRNA were designed using the siRNA design tool from the Whitehead Institute for Biomedical Research and ordered from Eurofins Genomics.
3
Knockdown of endogenous COQ7 transcripts
4
Identifying Anti-Apoptotic Genes
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The DAVID database was utilized to identify essential genes in the negative regulation of the apoptotic process. The findings were examined using the GeneMANIA database to identify the most significant genes in anti-apoptotic activities such as apoptotic signaling pathway negative regulation, intrinsic apoptotic signaling pathway negative regulation, and endothelial cell apoptotic process negative regulation. The Enrichr database was utilized to verify the acquired findings.
In this regard, the sequences of NFE2L2 and SIRT1 genes were collected from NCBI nucleotide [48 ]. To design siRNAs, Eurofins Genomic’s siRNA design tool was used, which is an online gadget providing the use of guidelines initially provided by Tuschl et al. [49 (link)]. In addition, it applies the scorings criteria [12 (link)] (including target site, length of siRNA, specificity checking, and nucleotide content of siRNA) developed by Reynolds et al. [50 (link)], Ui-Tei et al. [51 (link)], and Vert et al. [52 (link)]. To ensure the safety and prevent off-target effects of the designed siRNAs, the sequences were aligned by the human genome utilizing align sequences nucleotide BLAST [53 ].
In this regard, the sequences of NFE2L2 and SIRT1 genes were collected from NCBI nucleotide [48 ]. To design siRNAs, Eurofins Genomic’s siRNA design tool was used, which is an online gadget providing the use of guidelines initially provided by Tuschl et al. [49 (link)]. In addition, it applies the scorings criteria [12 (link)] (including target site, length of siRNA, specificity checking, and nucleotide content of siRNA) developed by Reynolds et al. [50 (link)], Ui-Tei et al. [51 (link)], and Vert et al. [52 (link)]. To ensure the safety and prevent off-target effects of the designed siRNAs, the sequences were aligned by the human genome utilizing align sequences nucleotide BLAST [53 ].
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