esiRNA non-coding mouse

The esiRNA technology is a powerful tool for loss of function gene studies. To illustrate the potency of silencing triggers quantitative real time (qRT)-PCR is often used to measure the knockdown rates. The knockdown validation on mRNA level was here performed 24 hours post transfection of esiRNA using qRT-PCR. To be able to assess knockdown rates, the expression levels of the mRNA of interest was compared to cells (HeLa or mouse ES) simultaneously transfected with Renilla Luciferase (negative control).

However, a more valuable measure of the knockdown potency in an RNAi experiment is the reduction in protein level. We therefore also validate the knockdown rates of esiRNAs on protein level using quantitative western blot analysis (Odyssey, Li-COR). The time point for maximum knockdown rate for each protein can vary significantly, as it is depending on factors such as protein stability, turnover rate or cell proliferation rates. The knockdown validation on protein level was here performed at 72 hours post transfection of esiRNA in HeLa cells. To be able to assess knockdown rates, the expression levels of the protein of interest was compared to HeLa cells simultaneously transfected with Renilla Luciferase (negative control). 

Two approaches were used to monitor knockdown at protein level: 1. Specific antibodies for the protein of interest were used for the quantitative western blot analysis. 2. Proteins of interest were GFP-tagged on a bacterial artificial chromosome (BAC) and stably integrated into the genome of HeLa cells, allowing for near physiological expression (Poser I. et al Nat Methods. 2008 May;5(5):409-15). Using a GFP antibody the detection by quantitative western blot analysis of the protein of interest is straightforward.

* Average of 2 technical replicates

esiRNA IDAccession No.LNC RNA NameLNC RNA DescriptionEnsembl IDRefSeq IDKnock-Down RatePDF
MNC-00089-1BC031453NR_046233.195,05 ± 1,66PDF
MNC-00018-1AK01835284,59 ± 2,18PDF
MNC-00010-1AF03213083,26 ± 8,18PDF
MNC-00060-1AK01232383,11 ± 0,08PDF
MNC-00063-1AK01851983,31 ± 0,91PDF
MNC-00087-1AK02035580,5 ± 12,19PDF
MNC-00173-1AK03327980,1 ± 1,17PDF
MNC-00492-1AK01699280 ± 6,6PDF
MNC-00102-1AK021247C430039J16RikRIKEN cDNA C430039J16 geneENSMUSG0000009145178,28 ± 2,97PDF
MNC-00114-1AK142231Rassf8Ras association (RalGDS/AF-6) domain family (N-terminal) member 8


78,19 ± 5,50PDF
MNC-00150-1AK02037277,46 ± 9,02PDF
MNC-00174-1AK01654476,03 ± 15,08PDF
MNC-00103-1AK0023902700038G22RikRIKEN cDNA 2700038G22 geneENSMUSG00000086802NR_045042.1
75,45 ± 7,92PDF
MNC-00127-1AK010004NR_027965.172,24 ± 1,63PDF
MNC-00139-1AK13159271,97 ± 13,21PDF
MNC-00163-1AK01462869,68 ± 6,78PDF
68,54 ± 14,96PDF
MNC-00105-1AK00870667,82 ± 5,18PDF
MNC-00190-1AK00790866,83 ± 6,30PDF
MNC-00192-1AK0185189030418K01RikRIKEN cDNA 9030418K01 geneENSMUSG0000007047666,73 ± 18,92PDF
MNC-00145-1AK004173Trmt61btRNA methyltransferase 61 homolog B (S. cerevisiae)ENSMUSG0000008549266,58 ± 20,09PDF
MNC-00169-1AK018410Cdc73cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)ENSMUSG0000002636166,42 ± 11,15PDF
MNC-00134-1AK0147144833417C18RikRIKEN cDNA 4833417C18 geneENSMUSG00000086015NR_045187.166,05 ± 16,15PDF
MNC-00386-1AK15655265,81 ± 8,13PDF
MNC-00232-1AK01554463,48 ± 7,82PDF
MNC-00210-1AK002866NR_040757.162,36 ± 4,60PDF
61,58 ± 8,96PDF