aedes albopictus c6 36 cells  (ATCC)


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    ATCC aedes albopictus c6 36 cells
    The insect cells <t>C6/36</t> (a) or the porcine cell line PEDSV.15 (b) were infected with a MOI of 0.01 TCID 50 /cell with P0 (blue), P1 (green), P5 (purple) or P10 (red) in triplicates. Passage lines B and C were depicted separately. The presence of the virus was analysed by RT-qPCR, as well as by titration on C6/36 and PEDSV.15 cells. Statistical significance was determined using Tukey’s multiple comparison test (ANOVA) using either the P0 values as reference (*p<0.05, **p<0.01; ***p<0.001; ****p<0.0001) or following exclusion of P0 using the P1 values as reference ( a p<0.05, aa p<0.01; aaa p<0.001; aaaa p<0.0001). The same colour code as above was used to indicate the affiliated groups.
    Aedes Albopictus C6 36 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Fitness adaptations of Japanese encephalitis virus in pigs following vector-free serial passaging"

    Article Title: Fitness adaptations of Japanese encephalitis virus in pigs following vector-free serial passaging

    Journal: bioRxiv

    doi: 10.1101/2024.02.20.581151

    The insect cells C6/36 (a) or the porcine cell line PEDSV.15 (b) were infected with a MOI of 0.01 TCID 50 /cell with P0 (blue), P1 (green), P5 (purple) or P10 (red) in triplicates. Passage lines B and C were depicted separately. The presence of the virus was analysed by RT-qPCR, as well as by titration on C6/36 and PEDSV.15 cells. Statistical significance was determined using Tukey’s multiple comparison test (ANOVA) using either the P0 values as reference (*p<0.05, **p<0.01; ***p<0.001; ****p<0.0001) or following exclusion of P0 using the P1 values as reference ( a p<0.05, aa p<0.01; aaa p<0.001; aaaa p<0.0001). The same colour code as above was used to indicate the affiliated groups.
    Figure Legend Snippet: The insect cells C6/36 (a) or the porcine cell line PEDSV.15 (b) were infected with a MOI of 0.01 TCID 50 /cell with P0 (blue), P1 (green), P5 (purple) or P10 (red) in triplicates. Passage lines B and C were depicted separately. The presence of the virus was analysed by RT-qPCR, as well as by titration on C6/36 and PEDSV.15 cells. Statistical significance was determined using Tukey’s multiple comparison test (ANOVA) using either the P0 values as reference (*p<0.05, **p<0.01; ***p<0.001; ****p<0.0001) or following exclusion of P0 using the P1 values as reference ( a p<0.05, aa p<0.01; aaa p<0.001; aaaa p<0.0001). The same colour code as above was used to indicate the affiliated groups.

    Techniques Used: Infection, Virus, Quantitative RT-PCR, Titration, Comparison

    aedes albopictus c6 36 cells  (ATCC)


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    ATCC aedes albopictus c6 36 cells
    Aedes Albopictus C6 36 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    aedes albopictus c6 36 cell  (ATCC)


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    ATCC aedes albopictus c6 36 cell
    Data sets and computational tools used for mapping SINV RNA modifications. ( A ) Read-level data features of full-length viral reads base called using the Dorado model. Baby hamster kidney BHK-21 and Aedes albopictus <t>C6/36</t> cells were infected with SINV at a multiplicity of infection of 0.1, followed by polyadenylated RNA isolation and ONT DRS. IVT RNA was synthesized from a plasmid encoding the SINV cDNA. Full-length viral reads were extracted from the alignment files. Read-level accuracy, identity, mismatch, insertion, and deletion were calculated using a custom Python script. ( B ) Base-level data features of full-length viral reads base called using the Dorado model. The confusion matrixes show the frequencies of each base being correctly base called, miscalled, or deleted in individual samples. ( C ) Classification of modification analysis tools used in the present study.
    Aedes Albopictus C6 36 Cell, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications"

    Article Title: Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications

    Journal: mSystems

    doi: 10.1128/msystems.01163-23

    Data sets and computational tools used for mapping SINV RNA modifications. ( A ) Read-level data features of full-length viral reads base called using the Dorado model. Baby hamster kidney BHK-21 and Aedes albopictus C6/36 cells were infected with SINV at a multiplicity of infection of 0.1, followed by polyadenylated RNA isolation and ONT DRS. IVT RNA was synthesized from a plasmid encoding the SINV cDNA. Full-length viral reads were extracted from the alignment files. Read-level accuracy, identity, mismatch, insertion, and deletion were calculated using a custom Python script. ( B ) Base-level data features of full-length viral reads base called using the Dorado model. The confusion matrixes show the frequencies of each base being correctly base called, miscalled, or deleted in individual samples. ( C ) Classification of modification analysis tools used in the present study.
    Figure Legend Snippet: Data sets and computational tools used for mapping SINV RNA modifications. ( A ) Read-level data features of full-length viral reads base called using the Dorado model. Baby hamster kidney BHK-21 and Aedes albopictus C6/36 cells were infected with SINV at a multiplicity of infection of 0.1, followed by polyadenylated RNA isolation and ONT DRS. IVT RNA was synthesized from a plasmid encoding the SINV cDNA. Full-length viral reads were extracted from the alignment files. Read-level accuracy, identity, mismatch, insertion, and deletion were calculated using a custom Python script. ( B ) Base-level data features of full-length viral reads base called using the Dorado model. The confusion matrixes show the frequencies of each base being correctly base called, miscalled, or deleted in individual samples. ( C ) Classification of modification analysis tools used in the present study.

    Techniques Used: Infection, Isolation, Synthesized, Plasmid Preparation, Modification

    Evaluation of 10 computational tools in detecting vRNA modifications with default or recommended parameters. ( A ) Correlations between probability values computed for the IVT and BHK-21 samples at each testable site using single-mode methods. ( B ) Correlations between probability values computed for the IVT and C6/36 samples. For panels A and B , equal numbers of reads were subsampled from individual data sets, followed by analyses using m6Anet, Nanom6A, and Tombo_de novo; all predictable A sites are included. ( C ) Workflow of identifying false-positive predictions resulting from comparative approaches. Briefly, full-length IVT reads were divided into two subsets and used as input data sets for comparison method analyses. The default or recommended cutoffs were applied, and the final predictions were regarded as false positives. ( D ) Volcano-like plot for output from error rate-based comparative method Differr. ( E ) Volcano-like plots for outputs from current signal-based comparative methods Tombo_com and Xpore. For panels D and E , dashed lines indicate recommended cutoff values; false-positive predictions are labeled in red; all types of modifications are included. FPR, false-positive rate. ( F ) Comparative tools with a FPR lower than 0.05%.
    Figure Legend Snippet: Evaluation of 10 computational tools in detecting vRNA modifications with default or recommended parameters. ( A ) Correlations between probability values computed for the IVT and BHK-21 samples at each testable site using single-mode methods. ( B ) Correlations between probability values computed for the IVT and C6/36 samples. For panels A and B , equal numbers of reads were subsampled from individual data sets, followed by analyses using m6Anet, Nanom6A, and Tombo_de novo; all predictable A sites are included. ( C ) Workflow of identifying false-positive predictions resulting from comparative approaches. Briefly, full-length IVT reads were divided into two subsets and used as input data sets for comparison method analyses. The default or recommended cutoffs were applied, and the final predictions were regarded as false positives. ( D ) Volcano-like plot for output from error rate-based comparative method Differr. ( E ) Volcano-like plots for outputs from current signal-based comparative methods Tombo_com and Xpore. For panels D and E , dashed lines indicate recommended cutoff values; false-positive predictions are labeled in red; all types of modifications are included. FPR, false-positive rate. ( F ) Comparative tools with a FPR lower than 0.05%.

    Techniques Used: Comparison, Labeling

    Integrated analysis of comparative methods. An equal number of reads, 772 in amount, were randomly subsampled from the BHK-21, C6/36, and IVT samples, followed by analyses using comparative methods. (A and B) UpSet plots for modification sites reported by different comparative methods in the BHK-21 or C6/36 samples. Red asterisks indicate significantly enriched intersections from the background. (C and D) Veen diagrams showing the intersections of Tombo_com and xPore predictions. The P -values were calculated by Fisher’s exact test. (E and F) Boxplots showing normalized signal differences at predicted modification sites and adjacent regions. The plots were generated using Tombo. Predicted sites are indicated by black arrows.
    Figure Legend Snippet: Integrated analysis of comparative methods. An equal number of reads, 772 in amount, were randomly subsampled from the BHK-21, C6/36, and IVT samples, followed by analyses using comparative methods. (A and B) UpSet plots for modification sites reported by different comparative methods in the BHK-21 or C6/36 samples. Red asterisks indicate significantly enriched intersections from the background. (C and D) Veen diagrams showing the intersections of Tombo_com and xPore predictions. The P -values were calculated by Fisher’s exact test. (E and F) Boxplots showing normalized signal differences at predicted modification sites and adjacent regions. The plots were generated using Tombo. Predicted sites are indicated by black arrows.

    Techniques Used: Modification, Generated

    Predictions of modification sites in the gRNAs and sgRNAs. As many reads as possible were subsampled from the original sequencing data while maintaining balanced coverage depths for the input dataset pairs, followed by analysis using the Tombo_com and xPore pipeline. (A) Intersections of modification sites in the SINV gRNAs generated in BHK-21 and C6/36 cells. (B) Positions of predicted modification sites in the SINV gRNAs. Read coverage depths of individual analyses are indicated in parentheses. (C) Intersections of modification sites in the SINV sgRNAs, generated in BHK-21 and C6/36 cells. (D) Positions of modification sites in the SINV sgRNAs.
    Figure Legend Snippet: Predictions of modification sites in the gRNAs and sgRNAs. As many reads as possible were subsampled from the original sequencing data while maintaining balanced coverage depths for the input dataset pairs, followed by analysis using the Tombo_com and xPore pipeline. (A) Intersections of modification sites in the SINV gRNAs generated in BHK-21 and C6/36 cells. (B) Positions of predicted modification sites in the SINV gRNAs. Read coverage depths of individual analyses are indicated in parentheses. (C) Intersections of modification sites in the SINV sgRNAs, generated in BHK-21 and C6/36 cells. (D) Positions of modification sites in the SINV sgRNAs.

    Techniques Used: Modification, Sequencing, Generated

    aedes albopictus mosquito c6 36 cells  (ATCC)


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    ATCC aedes albopictus mosquito c6 36 cells
    Aedes Albopictus Mosquito C6 36 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    aedes albopictus mosquito c6 36 cells  (ATCC)


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    ATCC aedes albopictus mosquito c6 36 cells
    Aedes Albopictus Mosquito C6 36 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    aedes albopictus cells c6 36  (ATCC)


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    ATCC aedes albopictus cells c6 36
    Aedes Albopictus Cells C6 36, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    c6 36 aedes albopictus cell line  (ATCC)


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    ATCC c6 36 aedes albopictus cell line
    A) Viral titers in culture supernatants. <t>C6/36,</t> BHK-21, and Vero cells were infected at MOI 0.1 with D2Y98P (WT), N130Q or T209L NS1 mutants. Viral titers in the culture supernatants were measured by plaque assay and were expressed as mean ± SD of triplicates. The detection limit was set at 10 2 pfu/ml. B) sNS1 levels in culture supernatant. sNS1 concentrations were determined by ELISA. Results were expressed as mean ± SD of triplicates. C-G) IFNAR -/- mice were infected with 10exp6 PFU of each virus via the subcutaneous (sc.) route. C-E) Survival, body weight loss profile and clinical scores (n=10); 0 – healthy, 1 – ruffled fur, 2 – hunched back, 3 – lethargy, 4 – limb paralysis, 5 – mice displaying 30% weight loss (euthanasia). F) Viremia titers were determined at the indicated points by plaque assay (n=5). G) Systemic sNS1 levels were measured by ELISA (n=5). Data shown are representative of at least 2 independent biological repeats.
    C6 36 Aedes Albopictus Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "De-glycosylated non-structural protein 1 enhances dengue virus clearance by limiting PD-L1/PD-1 mediated T cell apoptosis"

    Article Title: De-glycosylated non-structural protein 1 enhances dengue virus clearance by limiting PD-L1/PD-1 mediated T cell apoptosis

    Journal: bioRxiv

    doi: 10.1101/2024.01.08.574590

    A) Viral titers in culture supernatants. C6/36, BHK-21, and Vero cells were infected at MOI 0.1 with D2Y98P (WT), N130Q or T209L NS1 mutants. Viral titers in the culture supernatants were measured by plaque assay and were expressed as mean ± SD of triplicates. The detection limit was set at 10 2 pfu/ml. B) sNS1 levels in culture supernatant. sNS1 concentrations were determined by ELISA. Results were expressed as mean ± SD of triplicates. C-G) IFNAR -/- mice were infected with 10exp6 PFU of each virus via the subcutaneous (sc.) route. C-E) Survival, body weight loss profile and clinical scores (n=10); 0 – healthy, 1 – ruffled fur, 2 – hunched back, 3 – lethargy, 4 – limb paralysis, 5 – mice displaying 30% weight loss (euthanasia). F) Viremia titers were determined at the indicated points by plaque assay (n=5). G) Systemic sNS1 levels were measured by ELISA (n=5). Data shown are representative of at least 2 independent biological repeats.
    Figure Legend Snippet: A) Viral titers in culture supernatants. C6/36, BHK-21, and Vero cells were infected at MOI 0.1 with D2Y98P (WT), N130Q or T209L NS1 mutants. Viral titers in the culture supernatants were measured by plaque assay and were expressed as mean ± SD of triplicates. The detection limit was set at 10 2 pfu/ml. B) sNS1 levels in culture supernatant. sNS1 concentrations were determined by ELISA. Results were expressed as mean ± SD of triplicates. C-G) IFNAR -/- mice were infected with 10exp6 PFU of each virus via the subcutaneous (sc.) route. C-E) Survival, body weight loss profile and clinical scores (n=10); 0 – healthy, 1 – ruffled fur, 2 – hunched back, 3 – lethargy, 4 – limb paralysis, 5 – mice displaying 30% weight loss (euthanasia). F) Viremia titers were determined at the indicated points by plaque assay (n=5). G) Systemic sNS1 levels were measured by ELISA (n=5). Data shown are representative of at least 2 independent biological repeats.

    Techniques Used: Infection, Plaque Assay, Enzyme-linked Immunosorbent Assay, Virus

    aedes albopictus cells c6 36  (ATCC)


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    ATCC aedes albopictus cells c6 36
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    c6 36 aedes albopictus cell line  (ATCC)


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    ATCC c6 36 aedes albopictus cell line
    C6 36 Aedes Albopictus Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    aedes albopictus c6 36 cells  (ATCC)


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    ATCC aedes albopictus c6 36 cells
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    ATCC aedes albopictus c6 36 cells
    The insect cells <t>C6/36</t> (a) or the porcine cell line PEDSV.15 (b) were infected with a MOI of 0.01 TCID 50 /cell with P0 (blue), P1 (green), P5 (purple) or P10 (red) in triplicates. Passage lines B and C were depicted separately. The presence of the virus was analysed by RT-qPCR, as well as by titration on C6/36 and PEDSV.15 cells. Statistical significance was determined using Tukey’s multiple comparison test (ANOVA) using either the P0 values as reference (*p<0.05, **p<0.01; ***p<0.001; ****p<0.0001) or following exclusion of P0 using the P1 values as reference ( a p<0.05, aa p<0.01; aaa p<0.001; aaaa p<0.0001). The same colour code as above was used to indicate the affiliated groups.
    Aedes Albopictus C6 36 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/aedes albopictus c6 36 cells/product/ATCC
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    ATCC aedes albopictus c6 36 cell
    Data sets and computational tools used for mapping SINV RNA modifications. ( A ) Read-level data features of full-length viral reads base called using the Dorado model. Baby hamster kidney BHK-21 and Aedes albopictus <t>C6/36</t> cells were infected with SINV at a multiplicity of infection of 0.1, followed by polyadenylated RNA isolation and ONT DRS. IVT RNA was synthesized from a plasmid encoding the SINV cDNA. Full-length viral reads were extracted from the alignment files. Read-level accuracy, identity, mismatch, insertion, and deletion were calculated using a custom Python script. ( B ) Base-level data features of full-length viral reads base called using the Dorado model. The confusion matrixes show the frequencies of each base being correctly base called, miscalled, or deleted in individual samples. ( C ) Classification of modification analysis tools used in the present study.
    Aedes Albopictus C6 36 Cell, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATCC aedes albopictus mosquito c6 36 cells
    Data sets and computational tools used for mapping SINV RNA modifications. ( A ) Read-level data features of full-length viral reads base called using the Dorado model. Baby hamster kidney BHK-21 and Aedes albopictus <t>C6/36</t> cells were infected with SINV at a multiplicity of infection of 0.1, followed by polyadenylated RNA isolation and ONT DRS. IVT RNA was synthesized from a plasmid encoding the SINV cDNA. Full-length viral reads were extracted from the alignment files. Read-level accuracy, identity, mismatch, insertion, and deletion were calculated using a custom Python script. ( B ) Base-level data features of full-length viral reads base called using the Dorado model. The confusion matrixes show the frequencies of each base being correctly base called, miscalled, or deleted in individual samples. ( C ) Classification of modification analysis tools used in the present study.
    Aedes Albopictus Mosquito C6 36 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/aedes albopictus mosquito c6 36 cells/product/ATCC
    Average 86 stars, based on 1 article reviews
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    ATCC aedes albopictus cells c6 36
    Data sets and computational tools used for mapping SINV RNA modifications. ( A ) Read-level data features of full-length viral reads base called using the Dorado model. Baby hamster kidney BHK-21 and Aedes albopictus <t>C6/36</t> cells were infected with SINV at a multiplicity of infection of 0.1, followed by polyadenylated RNA isolation and ONT DRS. IVT RNA was synthesized from a plasmid encoding the SINV cDNA. Full-length viral reads were extracted from the alignment files. Read-level accuracy, identity, mismatch, insertion, and deletion were calculated using a custom Python script. ( B ) Base-level data features of full-length viral reads base called using the Dorado model. The confusion matrixes show the frequencies of each base being correctly base called, miscalled, or deleted in individual samples. ( C ) Classification of modification analysis tools used in the present study.
    Aedes Albopictus Cells C6 36, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    ATCC c6 36 aedes albopictus cell line
    A) Viral titers in culture supernatants. <t>C6/36,</t> BHK-21, and Vero cells were infected at MOI 0.1 with D2Y98P (WT), N130Q or T209L NS1 mutants. Viral titers in the culture supernatants were measured by plaque assay and were expressed as mean ± SD of triplicates. The detection limit was set at 10 2 pfu/ml. B) sNS1 levels in culture supernatant. sNS1 concentrations were determined by ELISA. Results were expressed as mean ± SD of triplicates. C-G) IFNAR -/- mice were infected with 10exp6 PFU of each virus via the subcutaneous (sc.) route. C-E) Survival, body weight loss profile and clinical scores (n=10); 0 – healthy, 1 – ruffled fur, 2 – hunched back, 3 – lethargy, 4 – limb paralysis, 5 – mice displaying 30% weight loss (euthanasia). F) Viremia titers were determined at the indicated points by plaque assay (n=5). G) Systemic sNS1 levels were measured by ELISA (n=5). Data shown are representative of at least 2 independent biological repeats.
    C6 36 Aedes Albopictus Cell Line, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    The insect cells C6/36 (a) or the porcine cell line PEDSV.15 (b) were infected with a MOI of 0.01 TCID 50 /cell with P0 (blue), P1 (green), P5 (purple) or P10 (red) in triplicates. Passage lines B and C were depicted separately. The presence of the virus was analysed by RT-qPCR, as well as by titration on C6/36 and PEDSV.15 cells. Statistical significance was determined using Tukey’s multiple comparison test (ANOVA) using either the P0 values as reference (*p<0.05, **p<0.01; ***p<0.001; ****p<0.0001) or following exclusion of P0 using the P1 values as reference ( a p<0.05, aa p<0.01; aaa p<0.001; aaaa p<0.0001). The same colour code as above was used to indicate the affiliated groups.

    Journal: bioRxiv

    Article Title: Fitness adaptations of Japanese encephalitis virus in pigs following vector-free serial passaging

    doi: 10.1101/2024.02.20.581151

    Figure Lengend Snippet: The insect cells C6/36 (a) or the porcine cell line PEDSV.15 (b) were infected with a MOI of 0.01 TCID 50 /cell with P0 (blue), P1 (green), P5 (purple) or P10 (red) in triplicates. Passage lines B and C were depicted separately. The presence of the virus was analysed by RT-qPCR, as well as by titration on C6/36 and PEDSV.15 cells. Statistical significance was determined using Tukey’s multiple comparison test (ANOVA) using either the P0 values as reference (*p<0.05, **p<0.01; ***p<0.001; ****p<0.0001) or following exclusion of P0 using the P1 values as reference ( a p<0.05, aa p<0.01; aaa p<0.001; aaaa p<0.0001). The same colour code as above was used to indicate the affiliated groups.

    Article Snippet: Aedes albopictus C6/36 cells (ATCC) were cultured at 28°C and 5% CO 2.

    Techniques: Infection, Virus, Quantitative RT-PCR, Titration, Comparison

    Data sets and computational tools used for mapping SINV RNA modifications. ( A ) Read-level data features of full-length viral reads base called using the Dorado model. Baby hamster kidney BHK-21 and Aedes albopictus C6/36 cells were infected with SINV at a multiplicity of infection of 0.1, followed by polyadenylated RNA isolation and ONT DRS. IVT RNA was synthesized from a plasmid encoding the SINV cDNA. Full-length viral reads were extracted from the alignment files. Read-level accuracy, identity, mismatch, insertion, and deletion were calculated using a custom Python script. ( B ) Base-level data features of full-length viral reads base called using the Dorado model. The confusion matrixes show the frequencies of each base being correctly base called, miscalled, or deleted in individual samples. ( C ) Classification of modification analysis tools used in the present study.

    Journal: mSystems

    Article Title: Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications

    doi: 10.1128/msystems.01163-23

    Figure Lengend Snippet: Data sets and computational tools used for mapping SINV RNA modifications. ( A ) Read-level data features of full-length viral reads base called using the Dorado model. Baby hamster kidney BHK-21 and Aedes albopictus C6/36 cells were infected with SINV at a multiplicity of infection of 0.1, followed by polyadenylated RNA isolation and ONT DRS. IVT RNA was synthesized from a plasmid encoding the SINV cDNA. Full-length viral reads were extracted from the alignment files. Read-level accuracy, identity, mismatch, insertion, and deletion were calculated using a custom Python script. ( B ) Base-level data features of full-length viral reads base called using the Dorado model. The confusion matrixes show the frequencies of each base being correctly base called, miscalled, or deleted in individual samples. ( C ) Classification of modification analysis tools used in the present study.

    Article Snippet: Aedes albopictus C6/36 cell and baby hamster kidney BHK-21 cell were purchased from the American Type Culture Collection, Manassas, VA, USA.

    Techniques: Infection, Isolation, Synthesized, Plasmid Preparation, Modification

    Evaluation of 10 computational tools in detecting vRNA modifications with default or recommended parameters. ( A ) Correlations between probability values computed for the IVT and BHK-21 samples at each testable site using single-mode methods. ( B ) Correlations between probability values computed for the IVT and C6/36 samples. For panels A and B , equal numbers of reads were subsampled from individual data sets, followed by analyses using m6Anet, Nanom6A, and Tombo_de novo; all predictable A sites are included. ( C ) Workflow of identifying false-positive predictions resulting from comparative approaches. Briefly, full-length IVT reads were divided into two subsets and used as input data sets for comparison method analyses. The default or recommended cutoffs were applied, and the final predictions were regarded as false positives. ( D ) Volcano-like plot for output from error rate-based comparative method Differr. ( E ) Volcano-like plots for outputs from current signal-based comparative methods Tombo_com and Xpore. For panels D and E , dashed lines indicate recommended cutoff values; false-positive predictions are labeled in red; all types of modifications are included. FPR, false-positive rate. ( F ) Comparative tools with a FPR lower than 0.05%.

    Journal: mSystems

    Article Title: Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications

    doi: 10.1128/msystems.01163-23

    Figure Lengend Snippet: Evaluation of 10 computational tools in detecting vRNA modifications with default or recommended parameters. ( A ) Correlations between probability values computed for the IVT and BHK-21 samples at each testable site using single-mode methods. ( B ) Correlations between probability values computed for the IVT and C6/36 samples. For panels A and B , equal numbers of reads were subsampled from individual data sets, followed by analyses using m6Anet, Nanom6A, and Tombo_de novo; all predictable A sites are included. ( C ) Workflow of identifying false-positive predictions resulting from comparative approaches. Briefly, full-length IVT reads were divided into two subsets and used as input data sets for comparison method analyses. The default or recommended cutoffs were applied, and the final predictions were regarded as false positives. ( D ) Volcano-like plot for output from error rate-based comparative method Differr. ( E ) Volcano-like plots for outputs from current signal-based comparative methods Tombo_com and Xpore. For panels D and E , dashed lines indicate recommended cutoff values; false-positive predictions are labeled in red; all types of modifications are included. FPR, false-positive rate. ( F ) Comparative tools with a FPR lower than 0.05%.

    Article Snippet: Aedes albopictus C6/36 cell and baby hamster kidney BHK-21 cell were purchased from the American Type Culture Collection, Manassas, VA, USA.

    Techniques: Comparison, Labeling

    Integrated analysis of comparative methods. An equal number of reads, 772 in amount, were randomly subsampled from the BHK-21, C6/36, and IVT samples, followed by analyses using comparative methods. (A and B) UpSet plots for modification sites reported by different comparative methods in the BHK-21 or C6/36 samples. Red asterisks indicate significantly enriched intersections from the background. (C and D) Veen diagrams showing the intersections of Tombo_com and xPore predictions. The P -values were calculated by Fisher’s exact test. (E and F) Boxplots showing normalized signal differences at predicted modification sites and adjacent regions. The plots were generated using Tombo. Predicted sites are indicated by black arrows.

    Journal: mSystems

    Article Title: Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications

    doi: 10.1128/msystems.01163-23

    Figure Lengend Snippet: Integrated analysis of comparative methods. An equal number of reads, 772 in amount, were randomly subsampled from the BHK-21, C6/36, and IVT samples, followed by analyses using comparative methods. (A and B) UpSet plots for modification sites reported by different comparative methods in the BHK-21 or C6/36 samples. Red asterisks indicate significantly enriched intersections from the background. (C and D) Veen diagrams showing the intersections of Tombo_com and xPore predictions. The P -values were calculated by Fisher’s exact test. (E and F) Boxplots showing normalized signal differences at predicted modification sites and adjacent regions. The plots were generated using Tombo. Predicted sites are indicated by black arrows.

    Article Snippet: Aedes albopictus C6/36 cell and baby hamster kidney BHK-21 cell were purchased from the American Type Culture Collection, Manassas, VA, USA.

    Techniques: Modification, Generated

    Predictions of modification sites in the gRNAs and sgRNAs. As many reads as possible were subsampled from the original sequencing data while maintaining balanced coverage depths for the input dataset pairs, followed by analysis using the Tombo_com and xPore pipeline. (A) Intersections of modification sites in the SINV gRNAs generated in BHK-21 and C6/36 cells. (B) Positions of predicted modification sites in the SINV gRNAs. Read coverage depths of individual analyses are indicated in parentheses. (C) Intersections of modification sites in the SINV sgRNAs, generated in BHK-21 and C6/36 cells. (D) Positions of modification sites in the SINV sgRNAs.

    Journal: mSystems

    Article Title: Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications

    doi: 10.1128/msystems.01163-23

    Figure Lengend Snippet: Predictions of modification sites in the gRNAs and sgRNAs. As many reads as possible were subsampled from the original sequencing data while maintaining balanced coverage depths for the input dataset pairs, followed by analysis using the Tombo_com and xPore pipeline. (A) Intersections of modification sites in the SINV gRNAs generated in BHK-21 and C6/36 cells. (B) Positions of predicted modification sites in the SINV gRNAs. Read coverage depths of individual analyses are indicated in parentheses. (C) Intersections of modification sites in the SINV sgRNAs, generated in BHK-21 and C6/36 cells. (D) Positions of modification sites in the SINV sgRNAs.

    Article Snippet: Aedes albopictus C6/36 cell and baby hamster kidney BHK-21 cell were purchased from the American Type Culture Collection, Manassas, VA, USA.

    Techniques: Modification, Sequencing, Generated

    A) Viral titers in culture supernatants. C6/36, BHK-21, and Vero cells were infected at MOI 0.1 with D2Y98P (WT), N130Q or T209L NS1 mutants. Viral titers in the culture supernatants were measured by plaque assay and were expressed as mean ± SD of triplicates. The detection limit was set at 10 2 pfu/ml. B) sNS1 levels in culture supernatant. sNS1 concentrations were determined by ELISA. Results were expressed as mean ± SD of triplicates. C-G) IFNAR -/- mice were infected with 10exp6 PFU of each virus via the subcutaneous (sc.) route. C-E) Survival, body weight loss profile and clinical scores (n=10); 0 – healthy, 1 – ruffled fur, 2 – hunched back, 3 – lethargy, 4 – limb paralysis, 5 – mice displaying 30% weight loss (euthanasia). F) Viremia titers were determined at the indicated points by plaque assay (n=5). G) Systemic sNS1 levels were measured by ELISA (n=5). Data shown are representative of at least 2 independent biological repeats.

    Journal: bioRxiv

    Article Title: De-glycosylated non-structural protein 1 enhances dengue virus clearance by limiting PD-L1/PD-1 mediated T cell apoptosis

    doi: 10.1101/2024.01.08.574590

    Figure Lengend Snippet: A) Viral titers in culture supernatants. C6/36, BHK-21, and Vero cells were infected at MOI 0.1 with D2Y98P (WT), N130Q or T209L NS1 mutants. Viral titers in the culture supernatants were measured by plaque assay and were expressed as mean ± SD of triplicates. The detection limit was set at 10 2 pfu/ml. B) sNS1 levels in culture supernatant. sNS1 concentrations were determined by ELISA. Results were expressed as mean ± SD of triplicates. C-G) IFNAR -/- mice were infected with 10exp6 PFU of each virus via the subcutaneous (sc.) route. C-E) Survival, body weight loss profile and clinical scores (n=10); 0 – healthy, 1 – ruffled fur, 2 – hunched back, 3 – lethargy, 4 – limb paralysis, 5 – mice displaying 30% weight loss (euthanasia). F) Viremia titers were determined at the indicated points by plaque assay (n=5). G) Systemic sNS1 levels were measured by ELISA (n=5). Data shown are representative of at least 2 independent biological repeats.

    Article Snippet: C6/36 Aedes albopictus cell line (ATCC; CRL-1660) was maintained in Leibotvitz’s L-15 medium (Gibco) supplemented with 10% FBS (Gibco) at 28 °C.

    Techniques: Infection, Plaque Assay, Enzyme-linked Immunosorbent Assay, Virus