esiRNA coding human

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 knock-down rates. The knock-down validation on mRNA level was here performed 24 hours post transfection of esiRNA using qRT-PCR. To be able to assess knock-down 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 knock-down potency in an RNAi experiment is the reduction in protein level. We therefore also validate the knock-down rates of esiRNAs on protein level using quantitative western blot analysis (Odyssey, Li-COR). The time point for maximum knock-down rate for each protein can vary significantly, as it is depending on factors such as protein-stability, turn-over rate or cell proliferation rates. The knock-down validation on protein level was here performed at 72 hours post transfection of esiRNA in HeLa cells.  To be able to assess knock-down 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 knock-down 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.



esiRNA IDGene NameGene Description Ensembl ID RefSeq IDKnock-Down RatePic / PDF
EHU137921IQGAP1IQ motif containing GTPase activating protein 1ENSG00000140575 99%Pic / PDF
EHU003851SAMHD1 SAM domain and HD domain 1ENSG00000101347NM_015474.397%Pic / PDF
EHU033661PCSK1proprotein convertase subtilisin/kexin type 1ENSG00000175426NM_00043996%Pic / PDF
EHU088511HMBOX1homeobox containing 1ENSG00000147421NM_02456796%Pic / PDF
EHU061761CDK2cyclin-dependent kinase 2ENSG00000123374NM_001798.3
NM_052827.2
96%Pic / PDF
EHU005241TNFRSF11Btumor necrosis factor receptor superfamily, member 11bENSG00000164761NM_00254695%Pic / PDF
EHU009691RND3Rho family GTPase 3ENSG00000115963NM_00516895%Pic / PDF
EHU025841HDAC1histone deacetylase 1ENSG00000116478NM_00496495%Pic / PDF
EHU077631PCDH7 protocadherin 7ENSG00000169851 NM_032456.2
NM_001173523.1
NM_032457.3
NM_002589.2
95%Pic / PDF
EHU012331KIF20A              kinesin family member 20AENSG00000112984NM_005733.295%Pic / PDF
EHU151981HIF1Ahypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)ENSG00000100644 95%Pic / PDF
EHU030271MECP2methyl CpG binding protein 2 (Rett syndrome)ENSG00000169057NM_004992.394%

Pic / PDF

EHU061741BECN1beclin 1, autophagy relatedENSG00000126581NM_00376694% Pic / PDF
EHU153321CCND1cyclin D1ENSG00000110092NM_05305694%Pic / PDF
EHU058001CLU clusterinENSG00000120885NR_045494.1
NM_001831.3
NR_038335.1
94%Pic / PDF
EHU157781FLNA filamin A, alphaENSG00000196924 NM_001110556.1
NM_001456.3
94%Pic / PDF
EHU013561MSH2 mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli) ENSG00000095002 NM_001258281.1
NM_000251.2
94%Pic / PDF
EHU109061RNF2 ring finger protein 2ENSG00000121481NM_007212.394%Pic / PDF
EHU088001PICALMphosphatidylinositol binding clathrin assembly proteinENSG00000073921NM_001206946.1
NM_007166.3
NM_001008660.2
NM_001206947.1
92%Pic / PDF
EHU082131 FMR1fragile X mental retardation 1ENSG00000102081NM_001185082.1
NM_001185081.1
NR_033700.1
NM_001185076.1
NM_001185075.1
NR_033699.1
NM_002024.5
92%

Pic / PDF

EHU089141ATXN3ataxin 3ENSG00000066427

NM_030660
NM_004993

91%

Pic / PDF

EHU040791                     GSK3Aglycogen synthase kinase 3 alphaENSG00000105723NM_01988491%Pic / PDF
EHU066841EZRezrinENSG00000092820NM_001111077.1
NM_003379.4
91%Pic / PDF
EHU051531PPP1R35protein phosphatase 1, regulatory subunit 35 ENSG00000160813NM_145030.289%Pic / PDF
EHU134251SKP1 S-phase kinase-associated protein 1ENSG00000113558NM_170679.2
NM_006930.3
89%

Pic / PDF

EHU108251LAP3leucine aminopeptidase 3ENSG00000002549NM_015907.288%

Pic / PDF

EHU089521ATMataxia telangiectasia mutatedENSG00000149311NM_000051
NM_138292
87%Pic / PDF
EHU029261FANCD2 Fanconi anemia, complementation group D2ENSG00000144554 NM_001018115.1
NM_033084.3
87%Pic / PDF
EHU078021NCSTNnicastrinENSG00000162736 NM_015331.287%

Pic / PDF

EHU111271HNRNPA1 heterogeneous nuclear ribonucleoprotein A1ENSG00000135486NM_031157.286%Pic / PDF
EHU001651RAB2A RAB2A, member RAS oncogene familyENSG00000104388NM_002865.286%Pic / PDF
EHU043721NFKBIAnuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alphaENSG00000100906NM_02052985%Pic / PDF
EHU077371RHOAras homolog family member AENSG00000067560NM_00166485%Pic / PDF
EHU030431SNAI1snail homolog 1 (Drosophila)ENSG00000124216NM_005985 83%Pic / PDF
EHU040501UHRF1ubiquitin-like with PHD and ring finger domains 1ENSG00000034063 NM_001048201.1
NM_013282.3
83%

Pic / PDF

EHU037101CDC73cell division cycle 73, Paf1ENSG00000134371NM_024529.482%

Pic / PDF

EHU143071BAG3BCL2-associated athanogene 3ENSG00000151929 NM_004281.382%Pic / PDF
EHU026721PAK2p21 protein (Cdc42/Rac)-activated kinase 2ENSG00000180370NR_027053.1
NM_002577.4
82%Pic / PDF
EHU074611MAD2L1 MAD2 mitotic arrest deficient-like 1 (yeast)ENSG00000164109NM_002358.381%Pic / PDF
EHU080431NCLnucleolinENSG00000115053NM_005381.281%

Pic / PDF

EHU062481MAPK3mitogen-activated protein kinase 3ENSG00000102882NM_001040056
NM_002746
NM_001109891
81%Pic / PDF
EHU029451MME membrane metallo-endopeptidaseENSG00000196549 NM_007289.2
NM_007288.2
NM_000902.3
NM_007287.2
80%Pic / PDF
EHU073601CASP9caspase 9, apoptosis-related cysteine peptidaseENSG00000132906NM_001229,NM_03299678%Pic / PDF
EHU131101POLD1polymerase (DNA directed), delta 1, catalytic subunit 125kDaENSG00000062822 78%Pic / PDF
EHU085781ATG5ATG5 autophagy related 5ENSG00000057663NM_00484976%Pic / PDF
EHU155611KDRkinase insert domain receptor (a type III receptor tyrosine kinase)ENSG00000128052NM_00225376%Pic / PDF
EHU071991VCPvalosin containing proteinENSG00000165280 NM_007126.375%Pic / PDF
EHU141461RELAv-rel reticuloendotheliosis viral oncogene homolog A (avian)ENSG0000017303974%Pic / PDF
EHU113911XRCC6 X-ray repair complementing defective repair in Chinese hamster cells 6ENSG00000196419 NM_001469.373%Pic / PDF
EHU004651HNRNPUheterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)ENSG00000153187 NM_004501.3
NM_031844.2
72%Pic / PDF
EHU117241CDC42 cell division cycle 42 (GTP binding protein, 25kDa)ENSG00000070831

NM_044472.2
NM_001791.3
NM_001039802.1

70%

Pic / PDF

EHU100711TGM2 transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)ENSG00000198959 NM_004613.270%Pic / PDF
EHU065671HNRNPKheterogeneous nuclear ribonucleoprotein KENSG00000165119 NM_002140.3
NM_031262.2
NM_031263.2
68%Pic / PDF
EHU122201UBL5 ubiquitin-like 5ENSG00000198258 NM_024292.367%Pic / PDF
EHU093561MYCNv-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)ENSG00000134323NM_00537865%Pic / PDF
EHU156851CSNK2A1casein kinase 2, alpha 1 polypeptideENSG00000101266 NM_177560.2
NM_001895.3
NM_177559.2
NM_001256686.1
62%Pic / PDF
EHU107101PPIApeptidylprolyl isomerase A (cyclophilin A) ENSG00000196262 NM_021130.360%

Pic / PDF

IQGAP1 / IQ motif containing GTPase activating protein 1

HMBOX1 / homeobox containing 1

RND3 / Rho family GTPase 3

BECN1 / beclin 1, autophagy related

HIF1A / hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)

FLNA / filamin A, alpha

SAMHD1 / SAM domain and HD domain 1

CDK2 / cyclin-dependent kinase 2

HDAC1 / histone deacetylase 1

PCDH7 / protocadherin 7

CCND1 / cyclin D1

MSH2 / mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)

PCSK1 / proprotein convertase subtilisin/kexin type 1

TNFRSF11B / tumor necrosis factor receptor superfamily, member 11b

MECP2 / methyl CpG binding protein 2 (Rett syndrome)

KIF20A / kinesin family member 20A

CLU / clusterin

RNF2 / ring finger protein 2

PICALM / phosphatidylinositol binding clathrin assembly protein

GSK3A / glycogen synthase kinase 3 alpha

SKP1 / S-phase kinase-associated protein 1

FANCD2 / Fanconi anemia, complementation group D2

RAB2A / RAB2A, member RAS oncogene family

SNAI1 / snail homolog 1 (Drosophila)

BAG3 / BCL2-associated athanogene 3

FMR1 / fragile X mental retardation 1

EZR / ezrin

LAP3 / leucine aminopeptidase 3

NCSTN / nicastrin

NFKBIA / nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha

UHRF1 / ubiquitin-like with PHD and ring finger domains 1

PAK2 / p21 protein (Cdc42/Rac)-activated kinase 2

ATXN3 / ataxin 3

PPP1R35 / protein phosphatase 1, regulatory subunit 35

ATM / ataxia telangiectasia mutated

HNRNPA1 / heterogeneous nuclear ribonucleoprotein A1

RHOA / ras homolog family member A

CDC73 / cell division cycle 73, Paf1

MAD2L1 / MAD2 mitotic arrest deficient-like 1 (yeast)

NCL / nucleolin

CASP9 / caspase 9, apoptosis-related cysteine peptidase

KDR / kinase insert domain receptor (a type III receptor tyrosine kinase)

XRCC6 / X-ray repair complementing defective repair in Chinese hamster cells 6

TGM2 / transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)

MYCN / v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)

MAPK3 / mitogen-activated protein kinase 3

POLD1 / polymerase (DNA directed), delta 1, catalytic subunit 125kDa

VCP / valosin containing protein

HNRNPU / heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)

HNRNPK / heterogeneous nuclear ribonucleoprotein K

CSNK2A1 / casein kinase 2, alpha 1 polypeptide

MME / membrane metallo-endopeptidase

ATG5 / ATG5 autophagy related 5

RELA / v-rel reticuloendotheliosis viral oncogene homolog A (avian)

CDC42 / cell division cycle 42 (GTP binding protein, 25kDa)

UBL5 / ubiquitin-like 5

PPIA / peptidylprolyl isomerase A (cyclophilin A)