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Eggs electroporated with cytoplasmic Cystatin, β-Actin-dsRNA, buffer and irrelevant lacZ-dsRNA and the endogenous expression of target gene was checked using real time RT-PCR one week following electroporation.
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The annotation of tRNA genes was checked using tRNAscan version 1.21 [ 51].
The specificity of each primer to their target genes was checked using the BLASTN program of the cucumber genomic database.
The quality of the 16S rRNA gene sequences was checked using the multiple alignment CLUSTALW software package [ 37].
Results on differentially expressed genes were compared to 5 major expression studies available from the PubMed GEO project [ 14- 18] and evidence of independent validation of gene expression data was checked using the PubMed database.
To avoid unintentional silencing of non-targeted host cell genes, sequence homology was checked using a basic local alignment search tool (BLAST) search (http://blast.ncbi.nlm.nih.gov/Blast.cgi).nih.gov/Blast.cgi
The expression of the 128 identified hit genes in HeLa cells was checked using mRNA-seq data from the Morin et al. study and publicly available gene expression data from the study of Zhang et al. obtained from GEO database (data set accession GDS3581, sample GSM410912).
The stability of mRNA expression of three genes: serA, cbiM, ndk was checked using the geNorm VBA applet for Microsoft Excel [ 37] and were chosen as internal standard for normalization.
The functional activity of resulting dsRNAs was checked using an in vitro gene silencing technique.
cDNA quality was checked using ABL as a control gene.
Convergence was checked using Tracer.
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