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.

* Average of 3 biological replicates


esiRNA ID
Gene Name
Gene Description
Ensembl ID
RefSeq ID
Knock-Down RatePDF
EHU001191TSPAN6tetraspanin 6ENSG00000000003NM_00327098,42 ± 1,00PDF
EHU156271STX7syntaxin 7ENSG00000079950NM_00356998,1 ± 1,21PDF
EHU054111RPA1replication protein A1, 70kDaENSG00000132383NM_00294598,05 ± 0,54PDF
EHU135081C9orf80chromosome 9 open reading frame 80ENSG00000148153 NM_021218.198 ± 0,55PDF
EHU042991TERF2telomeric repeat binding factor 2ENSG00000132604NM_005652.397,4 ± 0,02PDF
EHU122721HMGA1high mobility group AT-hook 1ENSG00000137309NM_145905.2
NM_145901.2
NM_145902.2
NM_145899.2
NM_002131.3
NM_145903.2
97 ± 0,18PDF
EHU111271HNRNPA1heterogeneous nuclear ribonucleoprotein A1ENSG00000135486NM_031157.297 ± 0,45PDF
EHU108731VDAC3voltage-dependent anion channel 3ENSG00000078668NM_005662.6
NM_001135694.2
96,86 ± 0,87PDF
EHU013371 PFDN2 prefoldin subunit 2ENSG00000143256NM_012394.396,65 ± 1,42PDF
EHU070551MTRR5-methyltetrahydrofolate-homocysteine methyltransferase reductaseENSG00000124275NM_02401096,49 ± 0,63PDF
EHU049861ZCCHC24zinc finger, CCHC domain containing 24ENSG00000165424NM_15336796,46 ± 0,49PDF
EHU127091H3F3AH3 histone, family 3AENSG00000163041

NM_002107
NR_002315
NR_003933

96,45 ± 1PDF
EHU093011TPX2TPX2, microtubule-associated, homolog (Xenopus laevis)ENSG00000088325NM_01211296,39 ± 0,6PDF
EHU137031CETN2centrin, EF-hand protein, 2ENSG00000147400NM_004344.196,15 ± 1,9PDF
EHU081861MORF4L2mortality factor 4 like 2ENSG00000123562NM_001142432.1
NM_001142431.1
NM_001142430.1
NM_001142429.1
NM_001142428.1
NM_001142427.1
NM_001142426.1
NM_001142425.1
NM_001142424.1
NM_001142423.1
NM_001142422.1
NM_001142421.1
NM_001142420.1
NM_001142419.1
NM_001142418.1
NM_012286.2
96 ± 0,31PDF
EHU114381PSIP1PC4 and SFRS1 interacting protein 1ENSG00000164985NM_001128217.1
NM_021144.3
NM_033222.3
96 ± 1,43PDF
EHU075631TJP2tight junction protein 2 
(zona occludens 2)
ENSG00000119139 NM_001170414.2
NM_201629.3
NM_001170416.1
NM_001170415.1
NM_004817.3
NM_001170630.1
96 ± 2,19PDF
EHU019381CENPOcentromere protein OENSG00000138092NM_001199803 NM_02432294,55 ± 0,89PDF
EHU100591PTRHD1peptidyl-tRNA hydrolase domain containing 1ENSG00000184924NM_00101366394,33 ± 2,47PDF
EHU107711SNW1SNW domain containing 1ENSG00000100603NM_01224595,79 ± 1,65PDF
EHU035851DBT dihydrolipoamide branched chain transacylase E2ENSG00000137992NM_001918.394 ±1,96PDF
EHU098021USP39ubiquitin specific peptidase 39ENSG00000168883NM_001256728.1
NR_046347.1
NM_001256727.1
NM_001256726.1
NM_001256725.1
NM_006590.3
94 ±1,18PDF
EHU152131SEC13SEC13 homolog (S. cerevisiae)ENSG00000157020NM_183352.1
NR_024273.1
NR_024272.1
NM_001136232.1
93,83 ± 1,1PDF
EHU000041KDELR1KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1ENSG00000105438NM_006801.293,57 ± 2,69PDF
EHU075381ADAM17ADAM metallopeptidase domain 17ENSG00000151694NM_00318393,39 ± 5,6PDF
EHU066181TRAPPC6Atrafficking protein particle complex 6AENSG00000007255 NM_024108.193,37 ± 1,09PDF
EHU013891PIR pirin (iron-binding nuclear protein) ENSG00000087842NM_001018109.2
NM_003662.3
93,05 ± 1,43PDF
EHU066621ARID1AAT rich interactive domain 1A (SWI-like)ENSG00000117713 NM_006015.4
NM_139135.2
93 ± 2,54PDF
EHU054441EIF2S1 eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDaENSG00000134001 NM_004094.493 ± 0,7PDF
EHU011541GRSF1G-rich RNA sequence binding factor 1ENSG00000132463 NM_002092.3
NM_001098477.1
93 ± 1,4PDF
EHU114821TERF1telomeric repeat binding factor (NIMA-interacting) 1ENSG00000147601NM_017489.2
NM_003218.3
93 ± 0,74PDF
EHU066121KIF23kinesin family member 23ENSG00000137807NM_138555
NM_004856
92,94 ± 0,9PDF
EHU051011PLK1polo-like kinase 1ENSG00000166851NM_00503092,53 ± 1,96PDF
EHU147201DYNLL1dynein, light chain, LC8-type 1ENSG00000088986NM_003746.2
NM_001037495.1
NM_001037494.1
92,46 ± 0,37PDF
EHU048131PDK3pyruvate dehydrogenase kinase, isozyme 3ENSG00000067992NM_005391.4
NM_001142386.2
92,38 ± 1,65PDF
EHU107631RCC2regulator of chromosome condensation 2ENSG00000179051 NM_001136204.2
NM_018715.3
92 ± 1,39PDF
EHU096181SRRTserrate RNA effector molecule homolog (Arabidopsis)ENSG00000087087NM_001128854.1
NM_001128853.1
NM_001128852.1
NM_015908.5
92 ± 1,39PDF
EHU063791LMNAlamin AENSG00000160789NM_170707
NM_170708
NM_005572
91,96 ± 0,9PDF
EHU062901CHD4chromodomain helicase DNA binding protein 4ENSG00000111642NM_00127391,82 ± 0,66PDF
EHU108801ANAPC10anaphase promoting complex subunit 10ENSG00000164162NM_001256711.1
NM_001256710.1
NM_001256709.1
NM_001256708.1
NM_014885.4
NM_001256707.1
NM_001256706.1
91,62 ± 3,3PDF
EHU051011CPS1carbamoyl-phosphate synthase 1, mitochondrialENSG00000021826NM_001122634.2
NM_001875.4
NM_001122633.2
91,54 ± 1,76PDF
EHU080041BTG3 BTG family, member 3 ENSG00000154640NM_001130914.1
NM_006806.4
91,49 ± 1,35PDF
EHU109951NEK2NIMA (never in mitosis gene a)-related kinase 2ENSG00000117650NM_00249791,48 ± 1,4PDF
EHU105871HMGB2 high mobility group box 2ENSG00000164104 NM_001130689.1
NM_001130688.1
NM_002129.3
91  ± 1,82PDF
EHU074611MAD2L1MAD2 mitotic arrest deficient-like 1 (yeast)ENSG00000164109NM_00235890,95 ± 2,0PDF
EHU108151STAT5Asignal transducer and activator of transcription 5AENSG00000126561 NM_003152.390,92 ± 1,58PDF
EHU143981PPP2R3Cprotein phosphatase 2, regulatory subunit B'', gammaENSG00000092020NM_017917.290,92 ± 2,8PDF
EHU035551GTF2H3general transcription factor IIH, polypeptide 3, 34kDaENSG00000111358NM_00151690,55 ± 3,32PDF
EHU135241GSTCDglutathione S-transferase, C-terminal domain containingENSG00000138780NM_024751.3
NM_001031720.3
90,50 ± 3,35PDF
EHU093871AFTPHaftiphilinENSG00000119844NM_01765790,07 ± 6,23PDF
EHU064771CDK13 cyclin-dependent kinase 13ENSG00000065883NM_031267.3
NM_003718.4
89,66 ± 1,41PDF
EHU036541NDFIP2Nedd4 family interacting protein 2 ENSG00000102471NM_001161407.1
NM_019080.2
89,25 ± 1,43PDF
EHU098771HNRNPM heterogeneous nuclear ribonucleoprotein MENSG00000099783 NM_031203.3
NM_005968.4
89  ± 1,3PDF
EHU144561THAP11THAP domain containing 11ENSG00000168286NM_020457.288,82 ± 2,28PDF
EHU056411TUBG1tubulin, gamma 1ENSG00000131462NM_00107088,26 ± 0,9PDF
EHU086581DCTN2dynactin 2 (p50)ENSG00000175203NM_006400.4
NM_001261413.1
NM_001261412.1
87,83 ± 3,6PDF
EHU017621CCDC115coiled-coil domain containing 115ENSG00000136710NM_03235787,59 ± 2,52PDF
EHU042151KIF2Akinesin heavy chain member 2AENSG00000068796NM_001243953.1
NM_001243952.1
NM_004520.4
NM_001098511.2
87,5 ± 1,23PDF
EHU020351CEP76centrosomal protein 76kDaENSG00000101624NM_001271989 NM_02489987,33 ± 2,42PDF
EHU029991ANAPC1anaphase promoting complex subunit 1ENSG00000153107NM_02266287,26 ± 2,9PDF
EHU108911RAD21RAD21 homolog (S. pombe)ENSG00000164754NM_00626587,09 ± 3,7PDF
EHU049161SEH1LSEH1-like (S. cerevisiae)ENSG00000085415NM_00101343786,97 ± 3,0PDF
EHU078221CKAP5cytoskeleton associated protein 5ENSG00000175216NM_001008938
NM_014756
86,59 ± 3,6PDF
EHU088171SKA3spindle and kinetochore associated complex subunit 3ENSG00000165480NM_14506186,31 ± 6,87PDF
EHU156161NCAPGnon-SMC condensin I complex, subunit GENSG00000109805NM_02234686,26 ± 5,1PDF
EHU063201TACC3transforming, acidic coiled-coil containing protein 3ENSG00000013810NM_00634286,06 ± 2,2PDF
EHU020331IRS1insulin receptor substrate 1ENSG00000169047NM_00554485,98 ± 4,09PDF
EHU098081CENPAcentromere protein AENSG00000115163NM_001809
NM_001042426
85,56 ± 2,9PDF
EHU089311SHOC2soc-2 suppressor of clear homolog (C. elegans)ENSG00000108061NM_001269039.1
NM_007373.3
85,48 ± 1,79PDF
EHU003621WEE1WEE1 homolog (S. pombe)ENSG00000166483NM_00339085,39 ± 6,24PDF
EHU090811SMARCC2SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2ENSG00000139613 NM_139067.2
NM_003075.3
NM_001130420.1
85,36 ± 0,99PDF
EHU048011NUP37nucleoporin 37kDaENSG00000075188NM_02405785,04 ± 3,5PDF
EHU088061ZNF691zinc finger protein 691ENSG00000164011 NM_015911.3
NM_001242739.1
85  ± 1,86PDF
EHU073291TUBGCP3tubulin, gamma complex associated protein 3ENSG00000126216NM_00632284,19 ± 2,9PDF
EHU000261IPO8importin 8ENSG00000133704NM_001190995.1
NM_006390.3
84,66 ± 3,34PDF
EHU155151EP300E1A binding protein p300ENSG00000100393NM_001429.384,58 ± 1,99PDF
EHU071491EGFL7EGF-like-domain, multiple 7ENSG00000172889NM_016215 NM_20144684,44 ± 4,08PDF
EHU079911BTBD3BTB (POZ) domain containing 3ENSG00000132640NM_014962.2
NM_181443.1
84,41 ± 1,1PDF
EHU093651SUV39H2suppressor of variegation 3-9 homolog 2 (Drosophila)ENSG00000152455NM_02467084,18 ± 2,5PDF
EHU031291DKC1dyskeratosis congenita 1, dyskerinENSG00000130826NM_00136384 ± 0,35PDF
EHU111021STRAPserine/threonine kinase receptor associated proteinENSG00000023734NM_007178.384 ±  6,3PDF
EHU040581CETN3centrin, EF-hand protein, 3ENSG00000153140NM_00436583,96 ± 2,4PDF
EHU069691ANAPC5anaphase promoting complex subunit 5ENSG00000089053NM_01623783,93 ± 2,0PDF
EHU107921MSX2msh homeobox 2ENSG00000120149NM_002449.4
NR_002307.1
83,60 ± 6,12PDF
EHU155811FOXA1forkhead box A1ENSG00000129514NM_00449683,31 ± 7,96PDF
EHU010431SNNstanninENSG00000184602NM_00349883,29 ± 1,48PDF
EHU090081ZMYM4 zinc finger, MYM-type 4ENSG00000146463NM_005095.283,06 ± 6,64PDF
EHU001891INCENPinner centromere protein antigens 135ENSG00000149503NM_02023882,38 ± 8,4PDF
EHU028941CLASP1cytoplasmic linker associated protein 1ENSG00000074054NM_001207051.1
NM_001142274.1
NM_001142273.1
NM_015282.2
82,13 ± 4,5PDF
EHU019931KIF11kinesin family member 11ENSG00000138160 NM_004523.381,98  ± 2,97PDF
EHU009751SSBP1single-stranded DNA binding protein 1ENSG00000106028NM_00314381,91 ± 1,38PDF
EHU020691FLT3fms-related tyrosine kinase 3ENSG00000122025 NM_004119.280,98 ± 9,87PDF
EHU007261CCP110centriolar coiled coil protein 110kDaENSG00000103540NM_01471180,91 ± 5,1PDF
EHU094431EDC4enhancer of mRNA decapping 4ENSG00000038358NM_01432980,89 ± 4,3PDF
EHU045751ZNF362zinc finger protein 362ENSG00000160094NM_15249380,78 ± 1,52PDF
EHU023071FGF12fibroblast growth factor 12ENSG00000114279NM_02103278,74 ± 4,91PDF
EHU022361TPP1tripeptidyl peptidase IENSG00000166340NM_00039178,43 ± 3PDF
EHU043591MAP6D1MAP6 domain containing 1ENSG00000180834NM_02487177,66 ± 2,61PDF
EHU079091VPS41 vacuolar protein sorting 41 homolog (S. cerevisiae)ENSG00000006715NM_014396.3
NM_080631.3
77,46 ± 3,15PDF
EHU160291CREBZFCREB/ATF bZIP transcription factor ENSG00000137504NR_028027.1
NR_028026.1
NR_028025.1
NR_028024.1
NM_001039618.2
77,35 ± 4,06PDF
EHU001691PLK4polo-like kinase 4ENSG00000142731NM_01426476,84 ± 11,2PDF
EHU138431PPIL2peptidylprolyl isomerase (cyclophilin)-like 2ENSG00000100023NM_148176.2
NM_148175.2
NM_014337.3
76,65 ± 9,83PDF
EHU001471AURKBaurora kinase BENSG00000178999NM_00421776,62 ± 6,3PDF
EHU130771XK X-linked Kx blood group (McLeod syndrome)ENSG00000047597NM_021083.276,54 ± 7,7PDF
EHU059141NUMA1nuclear mitotic apparatus protein 1ENSG00000137497NM_00618575,52 ± 3,8PDF
EHU093421AIG1androgen-induced 1ENSG00000146416NM_016108.275,48 ± 8,86PDF
EHU001571AHDC1AT hook, DNA binding motif, containing 1ENSG00000126705NM_00102988273,92 ± 3,42PDF
EHU026711CEP192centrosomal protein 192kDaENSG00000101639NM_03214272,99 ± 6,0PDF
EHU153811NR2C2APnuclear receptor 2C2-associated proteinENSG00000184162NM_17688072,07 ± 3,98PDF
EHU119681ARL6IP6ADP-ribosylation-like factor 6 interacting protein 6ENSG00000177917NM_15252271,61 ± 3,73PDF
EHU051901GPR88G protein-coupled receptor 88ENSG00000181656NM_02204971,55 ± 2,02PDF
EHU036651STAT5B signal transducer and activator of transcription 5BENSG00000173757NM_012448.371,40 ± 7,43PDF
EHU136181MAP2K7mitogen-activated protein kinase kinase 7ENSG00000076984NM_14518570,45 ± 2,54PDF