rnai screen Search Results


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  • 99
    Thermo Fisher in vivo rnai screen shrnas
    In Vivo Rnai Screen Shrnas, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore rna interference library screen
    Rna Interference Library Screen, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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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    Boehringer Ingelheim rnai screening collaboration
    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 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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    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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    91
    Horizon Discovery high throughput rnai screen sirnas
    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.
    High Throughput Rnai Screen Sirnas, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 91/100, 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
    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.
    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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    Horizon Discovery genome wide rnai screen the human kinome collection
    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.
    Genome Wide Rnai Screen The Human Kinome Collection, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Lufkin genome wide 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.
    Genome Wide Rnai Screen, supplied by Lufkin, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc genome wide 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.
    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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    Genmed genome wide pooled 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.
    Genome Wide Pooled Rnai Screen, supplied by Genmed, used in various techniques. Bioz Stars score: 89/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Thermo Fisher drosophila rnai screening center
    CLAMP inhibits NELF recruitment to highly paused genes. Chromatin immunoprecipitation of NELF-B was performed from <t>S2</t> cells treated with either gfp control (blue) or clamp (green) <t>RNAi.</t> The values for log 2 -fold enrichment over Input are shown after normalizing internally to a control locus ( cg15570 ) that is unbound for CLAMP or NELF-B. These values were then normalized to Input to generate the log 2 -fold enrichment value. Three separate biological replicates were averaged and the standard error of the mean was calculated (error bars are +/- 1 S.E.M.). Significance was determined using Kruskal-Wallis test by ranks, where the asterisk indicates a p-value
    Drosophila Rnai Screening Center, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 23 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: 97/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Basler laboratory screened rnai transgene lines
    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**
    Laboratory Screened Rnai Transgene Lines, supplied by Basler, used in various techniques. Bioz Stars score: 92/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Source BioScience plc screening reagents ahringer rnai feeding 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**
    Screening Reagents Ahringer Rnai Feeding Library, supplied by Source BioScience plc, used in various techniques. Bioz Stars score: 89/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Merck & Co rna silencing based 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**
    Rna Silencing Based Screens, supplied by Merck & Co, 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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    Horizon Discovery rnai screening dharmacon lincode smartpool sirna library human nr lncrna refseq v54
    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 Screening Dharmacon Lincode Smartpool Sirna Library Human Nr Lncrna Refseq V54, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 91/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore rnai screening synthesized sirna libraries
    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 Screening Synthesized Sirna Libraries, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rnai screening the ambion silencer select 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 Screening The Ambion Silencer Select Library, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 6 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**
    Rnai Depletion Screens Sirna Sequences Targeting Crl5 Adaptors, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 94/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Novartis rnai pooled screening
    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 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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    Pfizer Inc rnai probe 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**
    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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    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

    CLAMP inhibits NELF recruitment to highly paused genes. Chromatin immunoprecipitation of NELF-B was performed from S2 cells treated with either gfp control (blue) or clamp (green) RNAi. The values for log 2 -fold enrichment over Input are shown after normalizing internally to a control locus ( cg15570 ) that is unbound for CLAMP or NELF-B. These values were then normalized to Input to generate the log 2 -fold enrichment value. Three separate biological replicates were averaged and the standard error of the mean was calculated (error bars are +/- 1 S.E.M.). Significance was determined using Kruskal-Wallis test by ranks, where the asterisk indicates a p-value

    Journal: PLoS ONE

    Article Title: The Drosophila CLAMP protein associates with diverse proteins on chromatin

    doi: 10.1371/journal.pone.0189772

    Figure Lengend Snippet: CLAMP inhibits NELF recruitment to highly paused genes. Chromatin immunoprecipitation of NELF-B was performed from S2 cells treated with either gfp control (blue) or clamp (green) RNAi. The values for log 2 -fold enrichment over Input are shown after normalizing internally to a control locus ( cg15570 ) that is unbound for CLAMP or NELF-B. These values were then normalized to Input to generate the log 2 -fold enrichment value. Three separate biological replicates were averaged and the standard error of the mean was calculated (error bars are +/- 1 S.E.M.). Significance was determined using Kruskal-Wallis test by ranks, where the asterisk indicates a p-value

    Article Snippet: Cell culture conditions Drosophila S2 and Kc167 modENCODE cell lines from the Drosophila RNAi Screening Center were maintained at 25°C in Schneider’s media (ThermoFisher Scientific) supplemented with 10% Fetal Bovine Serum and 3.5% Antibiotic-Antimyotic (ThermoFisher Scientific).

    Techniques: Chromatin Immunoprecipitation

    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