| GR00017-A-0 |
23019 |
|
CNOT1 |
CNOT1_siRNA-Single-1 |
35.97 |
Wnt reporter downregulated |
|
no |
|
Wnt signaling |
New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening. |
Major et al. |
2008 |
19001663 |
Cell line |
DLD-1 |
Wnt signaling |
Dual luciferase |
Custom-made library |
|
siRNA |
Percentage Wnt reporter activity |
np |
|
GR00017-A-0 |
23019 |
|
CNOT1 |
CNOT1_siRNA-Single-3 |
3.63 |
Wnt reporter downregulated |
|
no |
|
Wnt signaling |
New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening. |
Major et al. |
2008 |
19001663 |
Cell line |
DLD-1 |
Wnt signaling |
Dual luciferase |
Custom-made library |
|
siRNA |
Percentage Wnt reporter activity |
np |
|
GR00018-A-0 |
23019 |
|
CNOT1 |
v2HS_115260 |
-2.6 (0) |
Synthetic lethal with Ras |
|
no |
|
Synthetic lethal interaction with Ras |
A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. |
Luo et al. |
2009 |
19490893 |
Cell line |
DLD-1 |
Synthetic lethal interaction with Ras |
Micoarray hybridization |
shRNA-mir (G. Hannon) |
|
shRNA |
Log2 diff MUT-WT (and P-value) |
-0.7 (0.3) |
|
GR00018-A-0 |
23019 |
|
CNOT1 |
v2HS_115263 |
-1.25 (0.28) |
Synthetic lethal with Ras |
|
no |
|
Synthetic lethal interaction with Ras |
A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. |
Luo et al. |
2009 |
19490893 |
Cell line |
DLD-1 |
Synthetic lethal interaction with Ras |
Micoarray hybridization |
shRNA-mir (G. Hannon) |
|
shRNA |
Log2 diff MUT-WT (and P-value) |
-0.7 (0.3) |
|
GR00053-A |
23019 |
NM_016284 |
KIAA1007 |
np |
sp |
Increased gamma-H2AX phosphorylation |
|
no |
group 2 |
Genome stability |
A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. |
Paulsen et al. |
2009 |
19647519 |
Cell line |
HeLa |
gamma-H2AX phosphorylation and DNA content |
Fluorescence |
siARRAY human genome siRNA library |
Genome-wide |
siRNA |
p-value |
Complex criteria |
Confidence groupings from 4 to 1 (highest level of confidence in group 4) |
GR00054-A |
23019 |
NM_016284 |
KIAA1007 |
np |
0.819 |
none |
|
no |
|
Combinatorial effect with paclitaxel |
Synthetic lethal screen identification of chemosensitizer loci in cancer cells. |
Whitehurst et al. |
2007 |
17429401 |
Cell line |
NCI-H1155 |
Viability (synthetic lethal) |
ATP level |
# G-005000-01 |
Genome-wide |
siRNA |
Paclitaxel/control ratio |
Complex criteria |
Additional information about 87 high-confidence hits |
GR00056-A |
23019 |
NM_016284 |
KIAA1007 |
np |
1.295 |
none |
|
no |
|
Melanogenesis |
Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells. |
Ganesan et al. |
2008 |
19057677 |
Cell line |
MNT-1 |
Melanin protein expression and viability |
Absorbance and luminescence |
rp |
Genome-wide |
siRNA |
Normalized absorbance ratio |
> 2 standard deviations below mean |
Additional information about a secondary screen (retest to determine false-positive rate) |
GR00057-A-1 |
23019 |
NM_016284 |
KIAA1007 |
M-015369-00 |
-1.11 |
none |
|
no |
|
Wnt/beta-catenin pathway regulation (1) |
A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer. |
Tang et al. |
2008 |
18621708 |
Cell line |
HeLa |
Wnt pathway reporter |
Luminescence |
Human siArray siRNA library |
Genome-wide |
siRNA |
Z-score |
> 4 |
Screen without Wnt3A stimulation. Additional information about secondary screens (Dharmacon and Qiagen libraries). |
GR00057-A-2 |
23019 |
NM_016284 |
KIAA1007 |
M-015369-00 |
sp |
Downregulation of Wnt pathway after Wnt3A stimulation |
|
yes |
|
Wnt/beta-catenin pathway regulation (2) |
A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer. |
Tang et al. |
2008 |
18621708 |
Cell line |
HeLa |
Wnt pathway reporter |
Luminescence |
Human siArray siRNA library |
Genome-wide |
siRNA |
Complex, SP |
Complex criteria |
Screen with Wnt3A stimulation. Additional information about secondary screens (Dharmacon and Qiagen libraries). |
GR00180-A-1 |
23019 |
23019 |
CNOT1 |
PL-50055 |
0.353 |
none |
|
no |
|
Hepatitis C virus replication (1) |
A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. |
Tai et al. |
2009 |
19286138 |
Cell line |
Huh7/Rep-Feo |
HCV replicon RNA copy number |
Luminescence |
siARRAY Human Genome siRNA Library |
Genome-wide |
siRNA |
q-value |
Complex criteria |
|
GR00184-A-1 |
23019 |
NM_016284 |
CNOT1 |
M-015369-00 |
-2.3471146554716 |
Decreased POU5F1-GFP protein expression |
|
no |
|
Self-renewal and pluripotency in human embryonic stem cells (1) |
A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. |
Chia et al. |
2010 |
20953172 |
Cell line |
hESC H1 |
POU5F1 protein expression |
Fluorescence |
SMARTpool siRNA library |
Genome-wide |
siRNA |
Z-score |
< -2 |
|
GR00197-A-1 |
23019 |
23019 |
CNOT1 |
M-015369-00 |
0.945715373 |
none |
|
no |
|
Human papillomavirus oncogene expression regulation (1) |
Genome-wide siRNA screen identifies SMCX, EP400, and Brd4 as E2-dependent regulators of human papillomavirus oncogene expression. |
Smith et al. |
2010 |
20133580 |
Cell line |
C33A/BE2/18LCR c4 |
HPV18 LCR reporter activity |
Luminescence |
Human siGENOME SMARTpool library |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Phenotype strength according to Z-scores: weak: 2 - 3; moderate: 3 - 5; strong: > 5 |
GR00233-A-1 |
23019 |
23019 |
CNOT1 |
np |
np |
Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection |
|
yes |
siRNA pool validated |
Hepatitis C virus (HCV) infection (1) |
A genome-wide genetic screen for host factors required for hepatitis C virus propagation. |
Li et al. |
2009 |
19717417 |
Cell line |
Huh7.5.1 |
HCV core protein expression and DNA content after virus infection |
Fluorescence |
Human Genome siARRAY siRNA G-005000–05 |
Genome-wide |
siRNA |
Percentage of infected cells |
< |
|
GR00233-A-2 |
23019 |
23019 |
CNOT1 |
D-015369-04 |
0.17 |
Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection after direct virus infection |
|
no |
normalized cell number < 0.5 |
Hepatitis C virus (HCV) infection (2) |
A genome-wide genetic screen for host factors required for hepatitis C virus propagation. |
Li et al. |
2009 |
19717417 |
Cell line |
Huh7.5.1 |
HCV core protein expression and DNA content after direct virus infection |
Fluorescence |
siARRAY siRNA |
Selected genes |
siRNA |
Normalized percentage of infected cells |
< |
|
GR00233-A-2 |
23019 |
23019 |
CNOT1 |
D-015369-03 |
0.19 |
Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection after direct virus infection |
|
no |
|
Hepatitis C virus (HCV) infection (2) |
A genome-wide genetic screen for host factors required for hepatitis C virus propagation. |
Li et al. |
2009 |
19717417 |
Cell line |
Huh7.5.1 |
HCV core protein expression and DNA content after direct virus infection |
Fluorescence |
siARRAY siRNA |
Selected genes |
siRNA |
Normalized percentage of infected cells |
< |
|
GR00233-A-2 |
23019 |
23019 |
CNOT1 |
D-015369-02 |
0.3 |
Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection after direct virus infection |
|
no |
|
Hepatitis C virus (HCV) infection (2) |
A genome-wide genetic screen for host factors required for hepatitis C virus propagation. |
Li et al. |
2009 |
19717417 |
Cell line |
Huh7.5.1 |
HCV core protein expression and DNA content after direct virus infection |
Fluorescence |
siARRAY siRNA |
Selected genes |
siRNA |
Normalized percentage of infected cells |
< |
|
GR00233-A-2 |
23019 |
23019 |
CNOT1 |
D-015369-01 |
0.13 |
Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection after direct virus infection |
|
no |
|
Hepatitis C virus (HCV) infection (2) |
A genome-wide genetic screen for host factors required for hepatitis C virus propagation. |
Li et al. |
2009 |
19717417 |
Cell line |
Huh7.5.1 |
HCV core protein expression and DNA content after direct virus infection |
Fluorescence |
siARRAY siRNA |
Selected genes |
siRNA |
Normalized percentage of infected cells |
< |
|
GR00233-A-3 |
23019 |
23019 |
CNOT1 |
D-015369-04 |
0.07 |
Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection after viral supernatant infection |
|
no |
normalized cell number in screen part one < 0.5 |
Hepatitis C virus (HCV) infection (3) |
A genome-wide genetic screen for host factors required for hepatitis C virus propagation. |
Li et al. |
2009 |
19717417 |
Cell line |
Huh7.5.1 |
HCV core protein expression and DNA content after viral supernatant infection |
Fluorescence |
siARRAY siRNA |
Selected genes |
siRNA |
Normalized percentage of infected cells |
< |
|
GR00233-A-3 |
23019 |
23019 |
CNOT1 |
D-015369-03 |
0.13 |
Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection after viral supernatant infection |
|
no |
|
Hepatitis C virus (HCV) infection (3) |
A genome-wide genetic screen for host factors required for hepatitis C virus propagation. |
Li et al. |
2009 |
19717417 |
Cell line |
Huh7.5.1 |
HCV core protein expression and DNA content after viral supernatant infection |
Fluorescence |
siARRAY siRNA |
Selected genes |
siRNA |
Normalized percentage of infected cells |
< |
|
GR00233-A-3 |
23019 |
23019 |
CNOT1 |
D-015369-02 |
0.23 |
Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection after viral supernatant infection |
|
no |
|
Hepatitis C virus (HCV) infection (3) |
A genome-wide genetic screen for host factors required for hepatitis C virus propagation. |
Li et al. |
2009 |
19717417 |
Cell line |
Huh7.5.1 |
HCV core protein expression and DNA content after viral supernatant infection |
Fluorescence |
siARRAY siRNA |
Selected genes |
siRNA |
Normalized percentage of infected cells |
< |
|
GR00233-A-3 |
23019 |
23019 |
CNOT1 |
D-015369-01 |
0.04 |
Decreased JFH-1 genotype 2a Hepatitis C virus (HCV) infection after viral supernatant infection |
|
no |
|
Hepatitis C virus (HCV) infection (3) |
A genome-wide genetic screen for host factors required for hepatitis C virus propagation. |
Li et al. |
2009 |
19717417 |
Cell line |
Huh7.5.1 |
HCV core protein expression and DNA content after viral supernatant infection |
Fluorescence |
siARRAY siRNA |
Selected genes |
siRNA |
Normalized percentage of infected cells |
< |
|
GR00236-A-1 |
23019 |
23019 |
CNOT1 |
M-015369-00 |
0.805123575701207 |
none |
|
no |
|
Homologous recombination DNA double-strand break repair (HR-DSBR) (1) |
A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. |
Adamson et al. |
2012 |
22344029 |
Cell line |
DR-U2OS |
(HR-DSBR) DR-GFP reporter and DNA content |
Fluorescence |
Human siGENOME siRNA (G-005000-05) |
Genome-wide |
siRNA |
Relative HR ratio |
< ~0.4 OR > 1.88 |
Cutoff values correspond 2 standard deviations from the screen-wide mean |
GR00240-S-1 |
23019 |
NM_016284 |
KIAA1007 |
M-015369-00 |
-0.08 |
none |
|
yes |
|
TRAIL-induced apoptosis (1) |
A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. |
Kranz and Boutros |
2014 |
24442637 |
Cell line |
U251MG |
Viability |
Luminescence |
SMART-pool siRNA |
Genome-wide |
siRNA |
Z-score |
> 4 |
Author-submitted data |
GR00240-S-2 |
23019 |
NM_016284 |
KIAA1007 |
M-015369-00 |
-0.24 |
none |
|
no |
Z-score -0.3405 |
TRAIL-induced apoptosis (2) |
A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. |
Kranz and Boutros |
2014 |
24442637 |
Cell line |
U251MG |
Viability (synthetic lethal) |
Luminescence |
SMART-pool siRNA |
Genome-wide |
siRNA |
Differential score |
> 3.6 AND viability Z-score < 4 |
Author-submitted data. Z-scores from viability screen (1) are considered in score interpretation for this screen. |
GR00242-A-1 |
23019 |
NM_016284 |
KIAA1007 |
np |
sp |
none |
|
no |
|
Selective autophagy regulation (1) |
Image-based genome-wide siRNA screen identifies selective autophagy factors. |
Orvedahl et al. |
2011 |
22020285 |
Cell line |
HeLa/GFP-LC3 |
Sindbis virus (SIN) capsid SIN-mCherry.capsid and autophagosome GFP–LC3 protein expression |
Fluorescence |
siGenome |
Genome-wide |
siRNA |
Z-score |
Complex criteria |
|
GR00247-A-1 |
23019 |
|
CNOT1 |
np |
sp |
none |
|
|
rank: 1184 |
Regulation of FOXO1 nuclear localization (1) |
Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain. |
Senapedis et al. |
2011 |
21460183 |
Cell line |
U2OS |
EGFP-FOXO1a protein expression and DNA content |
Fluorescence |
Human Genome library |
Genome-wide |
siRNA |
Complex, sp |
Complex criteria |
|
GR00249-S |
23019 |
23019 |
KIAA1007 |
J-015369-09 |
0.84565 |
none |
|
no |
number of cells compared to control (%): 72.75 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00249-S |
23019 |
23019 |
KIAA1007 |
M-015369-00 |
0.55414 |
none |
|
no |
number of cells compared to control (%): 74.49 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00249-S |
23019 |
23019 |
CNOT1 |
s22842 |
1.79336 |
Increased vaccinia virus (VACV) infection |
|
no |
number of cells compared to control (%): 63.10 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00249-S |
23019 |
23019 |
CNOT1 |
s22843 |
0.66579 |
none |
|
no |
number of cells compared to control (%): 64.95 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00249-S |
23019 |
23019 |
CNOT1 |
s22844 |
-1.76098 |
Decreased viability |
|
no |
number of cells compared to control (%): 28.13 |
Vaccinia virus (VACV) infection |
Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. |
Sivan et al. |
2013 |
23401514 |
Cell line |
HeLa |
Vaccinia virus VACV IHD-J/GFP protein expression and DNA content |
Fluorescence |
Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus |
Genome-wide |
siRNA |
Z-score |
> |
Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %. |
GR00253-A |
23019 |
NM_016284 |
KIAA1007 |
np |
-1.243 |
none |
|
|
|
hepcidin regulation |
Unbiased RNAi screen for hepcidin regulators links hepcidin suppression to proliferative Ras/RAF and nutrient-dependent mTOR signaling. |
Mleczko-Sanecka et al. |
2014 |
24385536 |
Cell line |
Huh7 |
hepcidin::fluc mRNA expression |
Luminescence |
siGenome siARRAY SMARTpool |
Genome-wide |
siRNA |
Z-score |
> |
Cutoff < |
GR00255-A-1 |
23019 |
23019 |
CNOT1 |
TRCN0000136340, TRCN0000136514, TRCN0000136673, TRCN0000137172 |
1.280349785 |
none |
|
|
|
Negative genetic interactions (1) |
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. |
Vizeacoumar et al. |
2013 |
24104479 |
Cell line |
HCT116 |
shRNA abundance |
Microarray |
np |
Genome-wide |
shRNA |
differential Gene Activity Ranking Profile (dGARP) |
< -1.0 |
HCT116 BLM-/- and HCT116 BLM+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells) |
GR00255-A-2 |
23019 |
23019 |
CNOT1 |
TRCN0000136340, TRCN0000136514, TRCN0000136673, TRCN0000137172 |
-0.657015772 |
none |
|
|
|
Negative genetic interactions (2) |
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. |
Vizeacoumar et al. |
2013 |
24104479 |
Cell line |
HCT116 |
shRNA abundance |
Microarray |
np |
Genome-wide |
shRNA |
differential Gene Activity Ranking Profile (dGARP) |
< -1.0 |
HCT116 MUS81-/- and HCT116 MUS81+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells) |
GR00255-A-3 |
23019 |
23019 |
CNOT1 |
TRCN0000136340, TRCN0000136514, TRCN0000136673, TRCN0000137172 |
1.712343182 |
none |
|
|
|
Negative genetic interactions (3) |
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. |
Vizeacoumar et al. |
2013 |
24104479 |
Cell line |
HCT116 |
shRNA abundance |
Microarray |
np |
Genome-wide |
shRNA |
differential Gene Activity Ranking Profile (dGARP) |
< -1.2 |
HCT116 PTEN-/- and HCT116 PTEN+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells) |
GR00255-A-4 |
23019 |
23019 |
CNOT1 |
TRCN0000136340, TRCN0000136514, TRCN0000136673, TRCN0000137172 |
2.575626824 |
none |
|
|
|
Negative genetic interactions (4) |
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. |
Vizeacoumar et al. |
2013 |
24104479 |
Cell line |
HCT116 |
shRNA abundance |
Microarray |
np |
Genome-wide |
shRNA |
differential Gene Activity Ranking Profile (dGARP) |
< -1.2 |
HCT116 PTTG1-/- and HCT116 PTTG1+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells) |
GR00255-A-5 |
23019 |
23019 |
CNOT1 |
TRCN0000136340, TRCN0000136514, TRCN0000136673, TRCN0000137172 |
-1.04459267 |
Negative genetic interaction between KRASG13D/+ and KRAS+/- |
|
|
|
Negative genetic interactions (5) |
A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. |
Vizeacoumar et al. |
2013 |
24104479 |
Cell line |
HCT116 |
shRNA abundance |
Microarray |
np |
Genome-wide |
shRNA |
differential Gene Activity Ranking Profile (dGARP) |
< -0.8 |
HCT116 KRASG13D/- and HCT116 KRAS+/- cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells) |
GR00257-A-1 |
23019 |
|
cnot1 |
215704 |
sp |
Decreased viability (cell death) |
|
|
|
Cell division, migration and survival (1) |
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. |
Neumann et al. |
2010 |
20360735 |
Cell line |
HeLa |
H2B-GFP protein expression |
Fluorescence |
Mapped using ENSEMBL genome database version 27 |
Selected genes |
siRNA |
Complex, sp |
Complex criteria |
HeLa-H2B-GFP cells used. |
GR00300-A |
23019 |
|
CNOT1 |
TRCN0000136673, TRCN0000136340, TRCN0000137172, TRCN0000136514 |
0 |
none |
|
|
|
Combinatorial effect with RAF inhibitor PLX4720 |
A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition. |
Whittaker et al. |
2013 |
23288408 |
Cell line |
A375 |
shRNA abundance |
Sequencing |
TRC |
Genome-wide |
shRNA |
Number of shRNAs ranked Top1000 |
> 2 |
The A375 cell line used here harbours the BRAF V600E mutation and is therefore sensitive to RAF inhibitors. |
GR00303-A |
23019 |
NM_016284 |
KIAA1007 |
np |
-2.26 |
none |
|
|
|
Clear cell renal cell carcinoma (ccRCC) survival regulation |
Genome-wide RNA interference analysis of renal carcinoma survival regulators identifies MCT4 as a Warburg effect metabolic target |
Gerlinger et al. |
2012 |
22362593 |
Cell line |
VHL-deficient RCC4 |
Proliferation and Viability |
Fluorescence |
np |
Genome-wide |
siRNA |
Z-score |
< |
In the phenotype data duplicates were in the original document, which have been removed. |
GR00310-A-1 |
23019 |
23019 |
KIAA1007 |
np |
-3.66 |
Decreased Sindbis virus (SINV) infection |
|
|
|
Sindbis virus (SINV) infection (1) |
Genome-Wide RNAi Screen Identifies Novel Host Proteins Required for Alphavirus Entry |
Ooi et al. |
2013 |
24367265 |
Cell line |
U2OS |
Sindbis virus (SINV) reporter |
Luminescence |
Ambion Silencer V3 |
Genome-wide |
siRNA |
Z-score |
< -3 OR > 2 |
|
|
23019 |
23019 |
CNOT1 |
np |
42.4 |
none |
|
|
101,7% viability |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00313-A |
23019 |
NM_016284 |
CNOT1 |
np |
-0.66 |
none |
|
|
|
TNF-alpha pathway regulation |
A Genome-Wide RNA Interference Screen Identifies Caspase 4 as a Factor Required for Tumor Necrosis Factor Alpha Signaling. |
Nickles et al. |
2012 |
22733992 |
Cell line |
HEK293T |
NFkappaB pathway reporter |
Luminescence |
Qiagen |
Genome-wide |
siRNA |
Z-score |
< |
Additional filters were a reduction in firefly luciferase levels by at least 50% compared to the mean of the experiment and a concomitant reduction of renilla luciferase expression of not more than 30%. |
GR00327-A |
23019 |
4847 |
NDUFA13 |
CLL-H-017737 |
3.767520271702687 |
Increased shRNA abundance |
|
|
|
Tumor formation |
An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation |
Wolf et al. |
2013 |
24292671 |
Cell line |
SUM-149 |
shRNA abundance |
Next-generation sequencing |
Decipher library module 1 |
Selected genes |
shRNA |
Z-score |
> 2.24 |
Genes were scored as hit if at least 2 shRNAs scored as hit, see comment. |
GR00327-A |
23019 |
4847 |
NDUFA13 |
CLL-H-017740 |
-0.6809837497634755 |
none |
|
|
|
Tumor formation |
An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation |
Wolf et al. |
2013 |
24292671 |
Cell line |
SUM-149 |
shRNA abundance |
Next-generation sequencing |
Decipher library module 1 |
Selected genes |
shRNA |
Z-score |
> 2.24 |
Genes were scored as hit if at least 2 shRNAs scored as hit, see comment. |
GR00327-A |
23019 |
4847 |
NDUFA13 |
CLL-H-017739 |
0.7435268525430654 |
none |
|
|
|
Tumor formation |
An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation |
Wolf et al. |
2013 |
24292671 |
Cell line |
SUM-149 |
shRNA abundance |
Next-generation sequencing |
Decipher library module 1 |
Selected genes |
shRNA |
Z-score |
> 2.24 |
Genes were scored as hit if at least 2 shRNAs scored as hit, see comment. |
GR00327-A |
23019 |
4847 |
NDUFA13 |
CLL-H-017736 |
-0.22699733333069672 |
none |
|
|
|
Tumor formation |
An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation |
Wolf et al. |
2013 |
24292671 |
Cell line |
SUM-149 |
shRNA abundance |
Next-generation sequencing |
Decipher library module 1 |
Selected genes |
shRNA |
Z-score |
> 2.24 |
Genes were scored as hit if at least 2 shRNAs scored as hit, see comment. |
GR00327-A |
23019 |
4847 |
NDUFA13 |
CLL-H-017738 |
-0.5020402711305404 |
none |
|
|
|
Tumor formation |
An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation |
Wolf et al. |
2013 |
24292671 |
Cell line |
SUM-149 |
shRNA abundance |
Next-generation sequencing |
Decipher library module 1 |
Selected genes |
shRNA |
Z-score |
> 2.24 |
Genes were scored as hit if at least 2 shRNAs scored as hit, see comment. |
|
23019 |
23019 |
CNOT1 |
|
0.07 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00371-A-1 |
23019 |
23019 |
CNOT1 |
|
-1.07269536628 |
none |
|
|
Ambion |
Nanog expression in absence of bFGF and TGFbeta |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-2 |
23019 |
CNOT1 |
23019 |
|
1.51845695626 |
Increased Nanog expression |
|
|
Ambion |
Nanog expression in presence of TGFbeta inhibitor |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-3 |
23019 |
23019 |
CNOT1 |
|
-0.657252465004 |
none |
|
|
Ambion |
Nanog expression in presence of MEK inhibitor |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-4 |
23019 |
23019 |
CNOT1 |
|
0.938628105495 |
Increased Nanog expression |
|
|
Ambion |
Nanog expression in presence of PI3K inhibitor |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00371-A-5 |
23019 |
23019 |
CNOT1 |
|
-1.1994102835 |
none |
|
|
Ambion |
Nanog expression in presence of retinoic acid |
Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways |
Gonzales et al. |
2015 |
26232226 |
Cell line |
NANOG-GFP H1 hESC |
NANOG expression |
Fluorescence |
Dharmacon and Ambion |
Selected genes |
siRNA |
Z-score |
>1,25 OR >1,5 [in at least two replicates] |
Z-score shown is an average of the z-scores from the three replicates performed for each gene. In the "Comment" field, the siRNA library used for each particular gene is noted. |
GR00376-A-1 |
23019 |
23019 |
CNOT1 |
|
0.531566249 |
none |
|
|
|
Mitigators of SS1P-induced immunotoxicity |
Whole-genome RNAi screen highlights components of the endoplasmic reticulum/Golgi as a source of resistance to immunotoxin-mediated cytotoxicity |
Pasetto et al. |
2015 |
25713356 |
Cell line |
KB cells |
Viability |
Luminescence |
Ambion Silencer Select Version 4 |
Genome-wide |
siRNA |
RSA P-value |
<0.001 |
SS1P was applied in a "high dose", ≈EC90, 13 ng/ml. Cutoff was derived from data submitted to Pubchem (ID 1117281). Reagent sequences but no ID |
GR00376-A-2 |
23019 |
23019 |
CNOT1 |
|
0.899296257 |
none |
|
|
|
Sensitizers of SS1P-induced immunotoxicity |
Whole-genome RNAi screen highlights components of the endoplasmic reticulum/Golgi as a source of resistance to immunotoxin-mediated cytotoxicity |
Pasetto et al. |
2015 |
25713356 |
Cell line |
KB cells |
Viability |
Luminescence |
Ambion Silencer Select Version 4 |
Genome-wide |
siRNA |
RSA P-value |
<0.001 |
SS1P was applied in a "low dose", ≈EC30, 3 ng/ml. Cutoff was derived from data submitted to PubChem (ID 1117281). Reagent sequences but no ID |
|
23019 |
NM_016284 |
CNOT1 |
|
42.896 |
none |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
GR00386-A-1 |
23019 |
23019 |
CNOT1 |
|
97.5203940457796 |
none |
|
|
|
NOD2 stimulation by MDP |
A genome-wide small interfering RNA (siRNA) screen reveals nuclear factor-κB (NF-κB)-independent regulators of NOD2-induced interleukin-8 (IL-8) secretion. |
Warner et al. |
2014 |
25170077 |
Cell line |
HEK293 stably expressing NOD2 |
Viability |
Luminescence |
Dharmacon |
Genome-wide |
siRNA |
Percentage growth |
Decreased: <70, increased: >120 |
Reagent IDs not provided |
GR00386-A-2 |
23019 |
23019 |
CNOT1 |
|
-1958.7 |
Increased IL-8 secretion |
|
|
Validated IL8 neg reg |
MDP-induced IL-8 secretion |
A genome-wide small interfering RNA (siRNA) screen reveals nuclear factor-κB (NF-κB)-independent regulators of NOD2-induced interleukin-8 (IL-8) secretion. |
Warner et al. |
2014 |
25170077 |
Cell line |
HEK293 stably expressing NOD2 |
IL-8 secretion |
ELISA |
Dharmacon |
Genome-wide |
siRNA |
Percent inhibition of IL-8 secretion |
Increased: <-300, Decreased: >60 |
Concentration of IL-8 was measured from cell supernatants by sandwich ELISA. IL-8 values (pg/ml) were normalized to IL-8 secreted in cells treated with RIPK2-specific siRNA (100% inhibition) and non-targeting siRNA (0% inhibition). Secondary validating screen assessed 554 genes whose silencing affected MDP-induced IL-8 secretion in the primary screen. Final validated IL-8 regulators (positive or negative) are listed in the comments column. Reagent IDs not provided |