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 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 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