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  • 91
    Horizon Discovery rnai screen
    Validation of Vaccinia virus HFs. (a) Validation of primary screen hits using plaque assays. <t>siRNA</t> SMARTpools targeting five genes identified in the primary <t>RNAi</t> screen as modulating VACV growth (one anti-viral factor MAP3K14 and four pro-viral factors TRIP, PPAP2A, VPS52 and CCT7), and one non-specific SMARTpool (VP16) were transfected into HeLa cells and, after 48 h, infected at low MOI (0.05) with VACV-A5eGFP. At 12 h intervals, cells were collected and the amount of virus present calculated using a plaque assay. Results obtained in the primary RNAi screen are plotted on the right hand axis for comparison.
    Rnai Screen, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 91/100, based on 33 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Novartis rnai screens
    Validation of Vaccinia virus HFs. (a) Validation of primary screen hits using plaque assays. <t>siRNA</t> SMARTpools targeting five genes identified in the primary <t>RNAi</t> screen as modulating VACV growth (one anti-viral factor MAP3K14 and four pro-viral factors TRIP, PPAP2A, VPS52 and CCT7), and one non-specific SMARTpool (VP16) were transfected into HeLa cells and, after 48 h, infected at low MOI (0.05) with VACV-A5eGFP. At 12 h intervals, cells were collected and the amount of virus present calculated using a plaque assay. Results obtained in the primary RNAi screen are plotted on the right hand axis for comparison.
    Rnai Screens, supplied by Novartis, used in various techniques. Bioz Stars score: 93/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Novartis large scale rna interference rnai screening data
    Validation of Vaccinia virus HFs. (a) Validation of primary screen hits using plaque assays. <t>siRNA</t> SMARTpools targeting five genes identified in the primary <t>RNAi</t> screen as modulating VACV growth (one anti-viral factor MAP3K14 and four pro-viral factors TRIP, PPAP2A, VPS52 and CCT7), and one non-specific SMARTpool (VP16) were transfected into HeLa cells and, after 48 h, infected at low MOI (0.05) with VACV-A5eGFP. At 12 h intervals, cells were collected and the amount of virus present calculated using a plaque assay. Results obtained in the primary RNAi screen are plotted on the right hand axis for comparison.
    Large Scale Rna Interference Rnai Screening Data, supplied by Novartis, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher rnai screen
    CDK4/6 Interference Sensitizes AML Cells toward Inhibition of Mutated KIT (A) Fold change of all KIT <t>shRNA</t> constructs in <t>RNAi</t> screens after third replatings (top) and in vivo engraftment (bottom) in t(8;21) cell lines. (B) String-generated gene network showing interactions between genes indicated by the in vivo RNAi screen. Nodes represent genes indicated by at least two shRNAs in combined SKNO-1 and Kasumi-1 screens. (C) Dose-response curves for proliferation of Kasumi-1 and SKNO-1 cells with palbociclib, imatinib (blue curves), or a combination with a fixed molar ratio of palboclib:imatinib of 1:10 (red curves). Top and bottom x axes show the corresponding palbociclib and imatinib concentrations. Cell numbers were counted after 72 hr of drug treatment. Mean ± SD; n = 4. See also Figure S8 .
    Rnai Screen, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 184 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    SourceForge net rnai screens
    CDK4/6 Interference Sensitizes AML Cells toward Inhibition of Mutated KIT (A) Fold change of all KIT <t>shRNA</t> constructs in <t>RNAi</t> screens after third replatings (top) and in vivo engraftment (bottom) in t(8;21) cell lines. (B) String-generated gene network showing interactions between genes indicated by the in vivo RNAi screen. Nodes represent genes indicated by at least two shRNAs in combined SKNO-1 and Kasumi-1 screens. (C) Dose-response curves for proliferation of Kasumi-1 and SKNO-1 cells with palbociclib, imatinib (blue curves), or a combination with a fixed molar ratio of palboclib:imatinib of 1:10 (red curves). Top and bottom x axes show the corresponding palbociclib and imatinib concentrations. Cell numbers were counted after 72 hr of drug treatment. Mean ± SD; n = 4. See also Figure S8 .
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    Merck & Co rna silencing based screens
    CDK4/6 Interference Sensitizes AML Cells toward Inhibition of Mutated KIT (A) Fold change of all KIT <t>shRNA</t> constructs in <t>RNAi</t> screens after third replatings (top) and in vivo engraftment (bottom) in t(8;21) cell lines. (B) String-generated gene network showing interactions between genes indicated by the in vivo RNAi screen. Nodes represent genes indicated by at least two shRNAs in combined SKNO-1 and Kasumi-1 screens. (C) Dose-response curves for proliferation of Kasumi-1 and SKNO-1 cells with palbociclib, imatinib (blue curves), or a combination with a fixed molar ratio of palboclib:imatinib of 1:10 (red curves). Top and bottom x axes show the corresponding palbociclib and imatinib concentrations. Cell numbers were counted after 72 hr of drug treatment. Mean ± SD; n = 4. See also Figure S8 .
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    89
    Horizon Discovery rnai screens
    CDK4/6 Interference Sensitizes AML Cells toward Inhibition of Mutated KIT (A) Fold change of all KIT <t>shRNA</t> constructs in <t>RNAi</t> screens after third replatings (top) and in vivo engraftment (bottom) in t(8;21) cell lines. (B) String-generated gene network showing interactions between genes indicated by the in vivo RNAi screen. Nodes represent genes indicated by at least two shRNAs in combined SKNO-1 and Kasumi-1 screens. (C) Dose-response curves for proliferation of Kasumi-1 and SKNO-1 cells with palbociclib, imatinib (blue curves), or a combination with a fixed molar ratio of palboclib:imatinib of 1:10 (red curves). Top and bottom x axes show the corresponding palbociclib and imatinib concentrations. Cell numbers were counted after 72 hr of drug treatment. Mean ± SD; n = 4. See also Figure S8 .
    Rnai Screens, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 89/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Horizon Discovery genome wide arrayed rnai screen
    CDK4/6 Interference Sensitizes AML Cells toward Inhibition of Mutated KIT (A) Fold change of all KIT <t>shRNA</t> constructs in <t>RNAi</t> screens after third replatings (top) and in vivo engraftment (bottom) in t(8;21) cell lines. (B) String-generated gene network showing interactions between genes indicated by the in vivo RNAi screen. Nodes represent genes indicated by at least two shRNAs in combined SKNO-1 and Kasumi-1 screens. (C) Dose-response curves for proliferation of Kasumi-1 and SKNO-1 cells with palbociclib, imatinib (blue curves), or a combination with a fixed molar ratio of palboclib:imatinib of 1:10 (red curves). Top and bottom x axes show the corresponding palbociclib and imatinib concentrations. Cell numbers were counted after 72 hr of drug treatment. Mean ± SD; n = 4. See also Figure S8 .
    Genome Wide Arrayed Rnai Screen, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 88/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Pfizer Inc rnai probe screens
    CDK4/6 Interference Sensitizes AML Cells toward Inhibition of Mutated KIT (A) Fold change of all KIT <t>shRNA</t> constructs in <t>RNAi</t> screens after third replatings (top) and in vivo engraftment (bottom) in t(8;21) cell lines. (B) String-generated gene network showing interactions between genes indicated by the in vivo RNAi screen. Nodes represent genes indicated by at least two shRNAs in combined SKNO-1 and Kasumi-1 screens. (C) Dose-response curves for proliferation of Kasumi-1 and SKNO-1 cells with palbociclib, imatinib (blue curves), or a combination with a fixed molar ratio of palboclib:imatinib of 1:10 (red curves). Top and bottom x axes show the corresponding palbociclib and imatinib concentrations. Cell numbers were counted after 72 hr of drug treatment. Mean ± SD; n = 4. See also Figure S8 .
    Rnai Probe Screens, supplied by Pfizer Inc, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Horizon Discovery rnai screen the sirna screen
    Graphical Overview of the Multiomic Approach to Charting the Transcription-Related DNA Damage Response UV-induced DNA damage has effects both at the local (“repairosome”) and the global level. The proteomic screens and the <t>siRNA</t> screen used to investigate the damage response are outlined. UV irradiation (30 J/m 2 ) was used for all proteomic analysis, while 15 J/m 2 was used in the <t>RNAi</t> screen.
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    Novartis rnai pooled screening
    Graphical Overview of the Multiomic Approach to Charting the Transcription-Related DNA Damage Response UV-induced DNA damage has effects both at the local (“repairosome”) and the global level. The proteomic screens and the <t>siRNA</t> screen used to investigate the damage response are outlined. UV irradiation (30 J/m 2 ) was used for all proteomic analysis, while 15 J/m 2 was used in the <t>RNAi</t> screen.
    Rnai Pooled Screening, supplied by Novartis, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Boehringer Ingelheim rnai screening collaboration
    Graphical Overview of the Multiomic Approach to Charting the Transcription-Related DNA Damage Response UV-induced DNA damage has effects both at the local (“repairosome”) and the global level. The proteomic screens and the <t>siRNA</t> screen used to investigate the damage response are outlined. UV irradiation (30 J/m 2 ) was used for all proteomic analysis, while 15 J/m 2 was used in the <t>RNAi</t> screen.
    Rnai Screening Collaboration, supplied by Boehringer Ingelheim, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher decode rnai viral screening library
    Graphical Overview of the Multiomic Approach to Charting the Transcription-Related DNA Damage Response UV-induced DNA damage has effects both at the local (“repairosome”) and the global level. The proteomic screens and the <t>siRNA</t> screen used to investigate the damage response are outlined. UV irradiation (30 J/m 2 ) was used for all proteomic analysis, while 15 J/m 2 was used in the <t>RNAi</t> screen.
    Decode Rnai Viral Screening Library, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Epigenomics recent epigenomics based genome wide rna interference rnai screens
    <t>RNAi</t> screens identify regulators of RAS silencing and regulators of RASSF1A <t>epigenetic</t> silencing. (A) RAS can inhibit FAS by DNA methylation-directed transcriptional repression. The components and mechanisms of this epigenetic repression were unknown.
    Recent Epigenomics Based Genome Wide Rna Interference Rnai Screens, supplied by Epigenomics, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Roche genome wide rnai screen
    <t>RNAi</t> screens identify regulators of RAS silencing and regulators of RASSF1A <t>epigenetic</t> silencing. (A) RAS can inhibit FAS by DNA methylation-directed transcriptional repression. The components and mechanisms of this epigenetic repression were unknown.
    Genome Wide Rnai Screen, supplied by Roche, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher human kinome rnai screen
    ALPK1 controls TIFA-mediated innate immunity during infection with invasive bacteria. A ) <t>Kinome</t> <t>RNAi</t> screening data of IL-8 expression after S . flexneri infection in HeLa cells. IL-8 measurements were extracted with CellProfiler, Z-scored and ranked. B ) Silencing TAK1 prevents S . flexneri -induced IL-8 expression but not TIFA oligomerization. Top panels show TIFA in green and S . flexneri in red. Bottom panels show F-actin in grey, DNA in blue, IL-8 in red and S . flexneri in green. Scale bars, 20 μm. C ) Silencing ALPK1 inhibits IL-8 expression induced by S . flexneri infection. Cells were transfected with control, TIFA and ALPK1-targeting siRNAs, infected and stained for IL-8. Data correspond to the mean +/- SD of three independent experiments, p**
    Human Kinome Rnai Screen, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Horizon Discovery rnai screen the sigenome human genome library
    ALPK1 controls TIFA-mediated innate immunity during infection with invasive bacteria. A ) <t>Kinome</t> <t>RNAi</t> screening data of IL-8 expression after S . flexneri infection in HeLa cells. IL-8 measurements were extracted with CellProfiler, Z-scored and ranked. B ) Silencing TAK1 prevents S . flexneri -induced IL-8 expression but not TIFA oligomerization. Top panels show TIFA in green and S . flexneri in red. Bottom panels show F-actin in grey, DNA in blue, IL-8 in red and S . flexneri in green. Scale bars, 20 μm. C ) Silencing ALPK1 inhibits IL-8 expression induced by S . flexneri infection. Cells were transfected with control, TIFA and ALPK1-targeting siRNAs, infected and stained for IL-8. Data correspond to the mean +/- SD of three independent experiments, p**
    Rnai Screen The Sigenome Human Genome Library, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Thermo Fisher rnai suppressor screen 1874 rnai clones
    ALPK1 controls TIFA-mediated innate immunity during infection with invasive bacteria. A ) <t>Kinome</t> <t>RNAi</t> screening data of IL-8 expression after S . flexneri infection in HeLa cells. IL-8 measurements were extracted with CellProfiler, Z-scored and ranked. B ) Silencing TAK1 prevents S . flexneri -induced IL-8 expression but not TIFA oligomerization. Top panels show TIFA in green and S . flexneri in red. Bottom panels show F-actin in grey, DNA in blue, IL-8 in red and S . flexneri in green. Scale bars, 20 μm. C ) Silencing ALPK1 inhibits IL-8 expression induced by S . flexneri infection. Cells were transfected with control, TIFA and ALPK1-targeting siRNAs, infected and stained for IL-8. Data correspond to the mean +/- SD of three independent experiments, p**
    Rnai Suppressor Screen 1874 Rnai Clones, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Greiner Bio rnai screen protocol glass bottom 96 well plates
    ALPK1 controls TIFA-mediated innate immunity during infection with invasive bacteria. A ) <t>Kinome</t> <t>RNAi</t> screening data of IL-8 expression after S . flexneri infection in HeLa cells. IL-8 measurements were extracted with CellProfiler, Z-scored and ranked. B ) Silencing TAK1 prevents S . flexneri -induced IL-8 expression but not TIFA oligomerization. Top panels show TIFA in green and S . flexneri in red. Bottom panels show F-actin in grey, DNA in blue, IL-8 in red and S . flexneri in green. Scale bars, 20 μm. C ) Silencing ALPK1 inhibits IL-8 expression induced by S . flexneri infection. Cells were transfected with control, TIFA and ALPK1-targeting siRNAs, infected and stained for IL-8. Data correspond to the mean +/- SD of three independent experiments, p**
    Rnai Screen Protocol Glass Bottom 96 Well Plates, supplied by Greiner Bio, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc genome wide rnai screens
    ALPK1 controls TIFA-mediated innate immunity during infection with invasive bacteria. A ) <t>Kinome</t> <t>RNAi</t> screening data of IL-8 expression after S . flexneri infection in HeLa cells. IL-8 measurements were extracted with CellProfiler, Z-scored and ranked. B ) Silencing TAK1 prevents S . flexneri -induced IL-8 expression but not TIFA oligomerization. Top panels show TIFA in green and S . flexneri in red. Bottom panels show F-actin in grey, DNA in blue, IL-8 in red and S . flexneri in green. Scale bars, 20 μm. C ) Silencing ALPK1 inhibits IL-8 expression induced by S . flexneri infection. Cells were transfected with control, TIFA and ALPK1-targeting siRNAs, infected and stained for IL-8. Data correspond to the mean +/- SD of three independent experiments, p**
    Genome Wide Rnai Screens, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Horizon Discovery rnai depletion screens sirna sequences targeting crl5 adaptors
    ALPK1 controls TIFA-mediated innate immunity during infection with invasive bacteria. A ) <t>Kinome</t> <t>RNAi</t> screening data of IL-8 expression after S . flexneri infection in HeLa cells. IL-8 measurements were extracted with CellProfiler, Z-scored and ranked. B ) Silencing TAK1 prevents S . flexneri -induced IL-8 expression but not TIFA oligomerization. Top panels show TIFA in green and S . flexneri in red. Bottom panels show F-actin in grey, DNA in blue, IL-8 in red and S . flexneri in green. Scale bars, 20 μm. C ) Silencing ALPK1 inhibits IL-8 expression induced by S . flexneri infection. Cells were transfected with control, TIFA and ALPK1-targeting siRNAs, infected and stained for IL-8. Data correspond to the mean +/- SD of three independent experiments, p**
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    Image Search Results


    Validation of Vaccinia virus HFs. (a) Validation of primary screen hits using plaque assays. siRNA SMARTpools targeting five genes identified in the primary RNAi screen as modulating VACV growth (one anti-viral factor MAP3K14 and four pro-viral factors TRIP, PPAP2A, VPS52 and CCT7), and one non-specific SMARTpool (VP16) were transfected into HeLa cells and, after 48 h, infected at low MOI (0.05) with VACV-A5eGFP. At 12 h intervals, cells were collected and the amount of virus present calculated using a plaque assay. Results obtained in the primary RNAi screen are plotted on the right hand axis for comparison.

    Journal: PLoS ONE

    Article Title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference

    doi: 10.1371/journal.pone.0098431

    Figure Lengend Snippet: Validation of Vaccinia virus HFs. (a) Validation of primary screen hits using plaque assays. siRNA SMARTpools targeting five genes identified in the primary RNAi screen as modulating VACV growth (one anti-viral factor MAP3K14 and four pro-viral factors TRIP, PPAP2A, VPS52 and CCT7), and one non-specific SMARTpool (VP16) were transfected into HeLa cells and, after 48 h, infected at low MOI (0.05) with VACV-A5eGFP. At 12 h intervals, cells were collected and the amount of virus present calculated using a plaque assay. Results obtained in the primary RNAi screen are plotted on the right hand axis for comparison.

    Article Snippet: RNA Interference Screen A schematic diagram of the workflow used in the RNAi screen is shown in . siRNA SMARTpools (4 siRNAs per gene, Dharmacon) were diluted to 0.3 µM and dispensed in 10 µl volumes using a Rapidplate384 liquid handler (Qiagen) into eight black 384-well plates (Corning).

    Techniques: Transfection, Infection, Plaque Assay

    Identification of HFs for Vaccinia virus replication by RNA interference screen. (a) Schematic of the experimental workflow used to screen the replication of VACV with the druggable RNAi library. (b) Comparison of the level of fluorescence of the control siRNAs used in the primary screen. Wells were transfected with siRNA targeting PRK-AB1 and eGFP (known to downregulate VACV-A5eGFP growth), two negative controls (mock transfection and RSCF siRNA) and two non-specific siRNAs (targeting VP16 or VP11/12 from Herpes simplex virus type 1). Error bars indicate the standard error of the mean. (c) Correlation between level of fluorescence and amount of virus present. HeLa cells were mock transfected or transfected with siRNA which is not processed by the RISC machinery (RSCF) or which knocks down a strong VACV pro-viral factor (FBXL11). After 48 h cells were infected with VACV-A5eGFP at low multiplicity of infection (MOI 0.05). At 24, 36 and 48 h post infection fluorescence was measured (y axis) before the cells were collected for titration using a plaque assay (x axis). Correlation (Pearson product moment correlation coefficient) between the two datasets = 0.86. (d) Plot of sorted z-scores representing the level of fluorescence associated with each of the 6 719 siRNA SMARTpools in the screen (average of 8 replicates). siRNA pools targeting genes of particular interest are marked.

    Journal: PLoS ONE

    Article Title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference

    doi: 10.1371/journal.pone.0098431

    Figure Lengend Snippet: Identification of HFs for Vaccinia virus replication by RNA interference screen. (a) Schematic of the experimental workflow used to screen the replication of VACV with the druggable RNAi library. (b) Comparison of the level of fluorescence of the control siRNAs used in the primary screen. Wells were transfected with siRNA targeting PRK-AB1 and eGFP (known to downregulate VACV-A5eGFP growth), two negative controls (mock transfection and RSCF siRNA) and two non-specific siRNAs (targeting VP16 or VP11/12 from Herpes simplex virus type 1). Error bars indicate the standard error of the mean. (c) Correlation between level of fluorescence and amount of virus present. HeLa cells were mock transfected or transfected with siRNA which is not processed by the RISC machinery (RSCF) or which knocks down a strong VACV pro-viral factor (FBXL11). After 48 h cells were infected with VACV-A5eGFP at low multiplicity of infection (MOI 0.05). At 24, 36 and 48 h post infection fluorescence was measured (y axis) before the cells were collected for titration using a plaque assay (x axis). Correlation (Pearson product moment correlation coefficient) between the two datasets = 0.86. (d) Plot of sorted z-scores representing the level of fluorescence associated with each of the 6 719 siRNA SMARTpools in the screen (average of 8 replicates). siRNA pools targeting genes of particular interest are marked.

    Article Snippet: RNA Interference Screen A schematic diagram of the workflow used in the RNAi screen is shown in . siRNA SMARTpools (4 siRNAs per gene, Dharmacon) were diluted to 0.3 µM and dispensed in 10 µl volumes using a Rapidplate384 liquid handler (Qiagen) into eight black 384-well plates (Corning).

    Techniques: Fluorescence, Transfection, Infection, Titration, Plaque Assay

    CDK4/6 Interference Sensitizes AML Cells toward Inhibition of Mutated KIT (A) Fold change of all KIT shRNA constructs in RNAi screens after third replatings (top) and in vivo engraftment (bottom) in t(8;21) cell lines. (B) String-generated gene network showing interactions between genes indicated by the in vivo RNAi screen. Nodes represent genes indicated by at least two shRNAs in combined SKNO-1 and Kasumi-1 screens. (C) Dose-response curves for proliferation of Kasumi-1 and SKNO-1 cells with palbociclib, imatinib (blue curves), or a combination with a fixed molar ratio of palboclib:imatinib of 1:10 (red curves). Top and bottom x axes show the corresponding palbociclib and imatinib concentrations. Cell numbers were counted after 72 hr of drug treatment. Mean ± SD; n = 4. See also Figure S8 .

    Journal: Cancer Cell

    Article Title: The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation

    doi: 10.1016/j.ccell.2018.08.015

    Figure Lengend Snippet: CDK4/6 Interference Sensitizes AML Cells toward Inhibition of Mutated KIT (A) Fold change of all KIT shRNA constructs in RNAi screens after third replatings (top) and in vivo engraftment (bottom) in t(8;21) cell lines. (B) String-generated gene network showing interactions between genes indicated by the in vivo RNAi screen. Nodes represent genes indicated by at least two shRNAs in combined SKNO-1 and Kasumi-1 screens. (C) Dose-response curves for proliferation of Kasumi-1 and SKNO-1 cells with palbociclib, imatinib (blue curves), or a combination with a fixed molar ratio of palboclib:imatinib of 1:10 (red curves). Top and bottom x axes show the corresponding palbociclib and imatinib concentrations. Cell numbers were counted after 72 hr of drug treatment. Mean ± SD; n = 4. See also Figure S8 .

    Article Snippet: RNAI Screen Library A customized shRNA library was purchased from Thermo Scientific. shRNAmir constructs that were unavailable as pTRIPZ constructs were cloned from pGIPZ to pTRIPZ as indicated by the provider (Thermo Scientific Open Biosystems Expression Arrest TRIPZ Lentiviral shRNAmir technical manual) with the exceptions of using Qiaprep Spin Miniprep Kit, Qiaquick Gel, Endofree Plasmid Maxi Kit and Qiaquick Gel Extraction Kit for the cloning stages and UltraClean Endotoxin-Free Mini plasmid Prep Kit to provide endotoxin free DNA plasmids.

    Techniques: Inhibition, shRNA, Construct, In Vivo, Generated

    A Combined In Vitro / In Vivo RNAi Screen Identifies CCND2 as Crucial Mediator of RUNX1/ETO Function (A) Scheme of the RNAi screen. t(8;21) cell lines were transduced with the lentiviral shRNA library and propagated with and without shRNA induction by doxycycline either in vitro in three consecutive replatings (12–14 days per plating) and long-term suspension culture for up to 56 days (LTC) or in vivo by xenotransplantation of immunodeficient mice killed upon reaching clinical endpoints. (B) Changes in relative (Rel.) sequencing read levels of proviral non-targeting control shRNA (shNTC) and RUNX1/ETO shRNA (shRE). (C) PCA of shRNA pools in Kasumi-1 colony formation assay (CFA) cells during replating. PC, principal component. (D) PCA of shRNA pools from Kasumi-1 transplanted NSG mice. dox, dox treatment initiated immediately after transplantation; dox delayed, doxycycline treatment initiated 28 days after transplantation. (E and F) Clustered heatmaps showing fold changes for genes in the in vitro (E) and the in vivo (F) arms of the RNAi screen. Fold changes were calculated based on collapsed changes of shRNAs using the RRA approach of MAGeCK. (G) Comparison of changes in shRNA construct levels in vivo and after the third replating. (H) Venn diagram identifying depleted shRNA constructs shared between the different RNAi screen conditions. (I and J) Fold change of all CCND2 shRNA constructs after third replatings (I) and in vivo engraftment (J). ∗∗∗ p

    Journal: Cancer Cell

    Article Title: The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation

    doi: 10.1016/j.ccell.2018.08.015

    Figure Lengend Snippet: A Combined In Vitro / In Vivo RNAi Screen Identifies CCND2 as Crucial Mediator of RUNX1/ETO Function (A) Scheme of the RNAi screen. t(8;21) cell lines were transduced with the lentiviral shRNA library and propagated with and without shRNA induction by doxycycline either in vitro in three consecutive replatings (12–14 days per plating) and long-term suspension culture for up to 56 days (LTC) or in vivo by xenotransplantation of immunodeficient mice killed upon reaching clinical endpoints. (B) Changes in relative (Rel.) sequencing read levels of proviral non-targeting control shRNA (shNTC) and RUNX1/ETO shRNA (shRE). (C) PCA of shRNA pools in Kasumi-1 colony formation assay (CFA) cells during replating. PC, principal component. (D) PCA of shRNA pools from Kasumi-1 transplanted NSG mice. dox, dox treatment initiated immediately after transplantation; dox delayed, doxycycline treatment initiated 28 days after transplantation. (E and F) Clustered heatmaps showing fold changes for genes in the in vitro (E) and the in vivo (F) arms of the RNAi screen. Fold changes were calculated based on collapsed changes of shRNAs using the RRA approach of MAGeCK. (G) Comparison of changes in shRNA construct levels in vivo and after the third replating. (H) Venn diagram identifying depleted shRNA constructs shared between the different RNAi screen conditions. (I and J) Fold change of all CCND2 shRNA constructs after third replatings (I) and in vivo engraftment (J). ∗∗∗ p

    Article Snippet: RNAI Screen Library A customized shRNA library was purchased from Thermo Scientific. shRNAmir constructs that were unavailable as pTRIPZ constructs were cloned from pGIPZ to pTRIPZ as indicated by the provider (Thermo Scientific Open Biosystems Expression Arrest TRIPZ Lentiviral shRNAmir technical manual) with the exceptions of using Qiaprep Spin Miniprep Kit, Qiaquick Gel, Endofree Plasmid Maxi Kit and Qiaquick Gel Extraction Kit for the cloning stages and UltraClean Endotoxin-Free Mini plasmid Prep Kit to provide endotoxin free DNA plasmids.

    Techniques: In Vitro, In Vivo, Transduction, shRNA, Mouse Assay, Sequencing, Colony Assay, Transplantation Assay, Construct

    Graphical Overview of the Multiomic Approach to Charting the Transcription-Related DNA Damage Response UV-induced DNA damage has effects both at the local (“repairosome”) and the global level. The proteomic screens and the siRNA screen used to investigate the damage response are outlined. UV irradiation (30 J/m 2 ) was used for all proteomic analysis, while 15 J/m 2 was used in the RNAi screen.

    Journal: Cell Reports

    Article Title: Multiomic Analysis of the UV-Induced DNA Damage Response

    doi: 10.1016/j.celrep.2016.04.047

    Figure Lengend Snippet: Graphical Overview of the Multiomic Approach to Charting the Transcription-Related DNA Damage Response UV-induced DNA damage has effects both at the local (“repairosome”) and the global level. The proteomic screens and the siRNA screen used to investigate the damage response are outlined. UV irradiation (30 J/m 2 ) was used for all proteomic analysis, while 15 J/m 2 was used in the RNAi screen.

    Article Snippet: RNAi Screen The siRNA screen was performed in MRC5VA cells with the Dharmacon Human siGENOME library.

    Techniques: Irradiation

    RNAi screens identify regulators of RAS silencing and regulators of RASSF1A epigenetic silencing. (A) RAS can inhibit FAS by DNA methylation-directed transcriptional repression. The components and mechanisms of this epigenetic repression were unknown.

    Journal: Genomics

    Article Title: Redefining regulation of DNA methylation by RNA interference

    doi: 10.1016/j.ygeno.2010.07.001

    Figure Lengend Snippet: RNAi screens identify regulators of RAS silencing and regulators of RASSF1A epigenetic silencing. (A) RAS can inhibit FAS by DNA methylation-directed transcriptional repression. The components and mechanisms of this epigenetic repression were unknown.

    Article Snippet: Subsequently, we discuss two recent epigenomics-based genome-wide RNA interference (RNAi) screens and show how these screens resulted in the identification of new pathways of epigenetic regulation in cancer [ , ].

    Techniques: DNA Methylation Assay

    Proposed RNAi screens to study imprinting or synthetic lethality in the context of an epigenetic change. (A) A proposed screen for identification of genes that regulate imprinting. This screen can be adapted to understand the regulation of any imprinted

    Journal: Genomics

    Article Title: Redefining regulation of DNA methylation by RNA interference

    doi: 10.1016/j.ygeno.2010.07.001

    Figure Lengend Snippet: Proposed RNAi screens to study imprinting or synthetic lethality in the context of an epigenetic change. (A) A proposed screen for identification of genes that regulate imprinting. This screen can be adapted to understand the regulation of any imprinted

    Article Snippet: Subsequently, we discuss two recent epigenomics-based genome-wide RNA interference (RNAi) screens and show how these screens resulted in the identification of new pathways of epigenetic regulation in cancer [ , ].

    Techniques:

    ALPK1 controls TIFA-mediated innate immunity during infection with invasive bacteria. A ) Kinome RNAi screening data of IL-8 expression after S . flexneri infection in HeLa cells. IL-8 measurements were extracted with CellProfiler, Z-scored and ranked. B ) Silencing TAK1 prevents S . flexneri -induced IL-8 expression but not TIFA oligomerization. Top panels show TIFA in green and S . flexneri in red. Bottom panels show F-actin in grey, DNA in blue, IL-8 in red and S . flexneri in green. Scale bars, 20 μm. C ) Silencing ALPK1 inhibits IL-8 expression induced by S . flexneri infection. Cells were transfected with control, TIFA and ALPK1-targeting siRNAs, infected and stained for IL-8. Data correspond to the mean +/- SD of three independent experiments, p**

    Journal: PLoS Pathogens

    Article Title: ALPK1 controls TIFA/TRAF6-dependent innate immunity against heptose-1,7-bisphosphate of gram-negative bacteria

    doi: 10.1371/journal.ppat.1006224

    Figure Lengend Snippet: ALPK1 controls TIFA-mediated innate immunity during infection with invasive bacteria. A ) Kinome RNAi screening data of IL-8 expression after S . flexneri infection in HeLa cells. IL-8 measurements were extracted with CellProfiler, Z-scored and ranked. B ) Silencing TAK1 prevents S . flexneri -induced IL-8 expression but not TIFA oligomerization. Top panels show TIFA in green and S . flexneri in red. Bottom panels show F-actin in grey, DNA in blue, IL-8 in red and S . flexneri in green. Scale bars, 20 μm. C ) Silencing ALPK1 inhibits IL-8 expression induced by S . flexneri infection. Cells were transfected with control, TIFA and ALPK1-targeting siRNAs, infected and stained for IL-8. Data correspond to the mean +/- SD of three independent experiments, p**

    Article Snippet: The human kinome RNAi screen was performed with the Ambion library made of three individual siRNAs per gene.

    Techniques: Infection, Expressing, Transfection, Staining