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chip seq high throughput sequencing  (Novogene)

 
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    Novogene chip seq high throughput sequencing
    a 293T cells were infected with WT or ICP0-null HSV-1 (MOI = 10) for 5 h before ChIP-qPCR analysis using an FOXF1 or FOXP1 antibody or an IgG control. b Neuro-2a cells were transfected with pFOXF1 (Flag-tagged) for 42 h, then infected (MOI = 5) for 5 h <t>before</t> <t>ChIP-seq</t> analysis using an anti-Flag antibody. Shown are coverage plots for reads aligned to the HSV-1 genome with terminal repeat regions deleted. Orange vertical sticks represent peaks. Green vertical sticks represent positions of RTAAACA or its complementary <t>sequence.</t> c Upper: the percentages of viral reads relative to total reads in the ChIP-seq data. Lower: Motif analysis of the ChIP-seq data. d N2AFOXF1 and N2Aempty cells were treated with DOX for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis of the indicated sites using an anti-Flag antibody. e N2A-FOXK1KO cells were transfected with pFOXK1 for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis as in ( d ). f Neuro-2a cells were transfected with 200 ng/mL of the indicated plasmids for 24 h before infection and virus titration. The P value represents the difference between each gene under the horizontal line and the control. g The crystal structure of the FOXC2 DBD with DNA was visualized using PyMOL software (PDB ID: 6AKO), with key interactions highlighted. h – j Transfection-infection experiments in Neuro-2a ( h , i ) or N2A-FOXK1KO cells ( j ) performed as in ( f ). k ChIP-qPCR analysis performed as in ( d ). All infections used ICP0-null HSV-1. Cells were infected (MOI = 0.2) for 48 h for ( f , h , i , and j ). n = 2 ( b , c ), 3 ( a , d , e , f , h , i , k ) or 4 ( j ) biologically independent samples. Data were analyzed by one-way ANOVA with Dunnett’s multiple comparisons tests ( a , f , h , i , j ) or two-way ANOVA with Sidak’s multiple comparisons tests ( d , e , k ) and are presented as mean ± SD. Source data are provided as a Source Data file.
    Chip Seq High Throughput Sequencing, supplied by Novogene, 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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    chip seq high throughput sequencing - by Bioz Stars, 2026-06
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    Images

    1) Product Images from "Counteracting FOX proteins epigenetically control the herpesvirus lytic-latent balance"

    Article Title: Counteracting FOX proteins epigenetically control the herpesvirus lytic-latent balance

    Journal: Nature Communications

    doi: 10.1038/s41467-026-68915-1

    a 293T cells were infected with WT or ICP0-null HSV-1 (MOI = 10) for 5 h before ChIP-qPCR analysis using an FOXF1 or FOXP1 antibody or an IgG control. b Neuro-2a cells were transfected with pFOXF1 (Flag-tagged) for 42 h, then infected (MOI = 5) for 5 h before ChIP-seq analysis using an anti-Flag antibody. Shown are coverage plots for reads aligned to the HSV-1 genome with terminal repeat regions deleted. Orange vertical sticks represent peaks. Green vertical sticks represent positions of RTAAACA or its complementary sequence. c Upper: the percentages of viral reads relative to total reads in the ChIP-seq data. Lower: Motif analysis of the ChIP-seq data. d N2AFOXF1 and N2Aempty cells were treated with DOX for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis of the indicated sites using an anti-Flag antibody. e N2A-FOXK1KO cells were transfected with pFOXK1 for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis as in ( d ). f Neuro-2a cells were transfected with 200 ng/mL of the indicated plasmids for 24 h before infection and virus titration. The P value represents the difference between each gene under the horizontal line and the control. g The crystal structure of the FOXC2 DBD with DNA was visualized using PyMOL software (PDB ID: 6AKO), with key interactions highlighted. h – j Transfection-infection experiments in Neuro-2a ( h , i ) or N2A-FOXK1KO cells ( j ) performed as in ( f ). k ChIP-qPCR analysis performed as in ( d ). All infections used ICP0-null HSV-1. Cells were infected (MOI = 0.2) for 48 h for ( f , h , i , and j ). n = 2 ( b , c ), 3 ( a , d , e , f , h , i , k ) or 4 ( j ) biologically independent samples. Data were analyzed by one-way ANOVA with Dunnett’s multiple comparisons tests ( a , f , h , i , j ) or two-way ANOVA with Sidak’s multiple comparisons tests ( d , e , k ) and are presented as mean ± SD. Source data are provided as a Source Data file.
    Figure Legend Snippet: a 293T cells were infected with WT or ICP0-null HSV-1 (MOI = 10) for 5 h before ChIP-qPCR analysis using an FOXF1 or FOXP1 antibody or an IgG control. b Neuro-2a cells were transfected with pFOXF1 (Flag-tagged) for 42 h, then infected (MOI = 5) for 5 h before ChIP-seq analysis using an anti-Flag antibody. Shown are coverage plots for reads aligned to the HSV-1 genome with terminal repeat regions deleted. Orange vertical sticks represent peaks. Green vertical sticks represent positions of RTAAACA or its complementary sequence. c Upper: the percentages of viral reads relative to total reads in the ChIP-seq data. Lower: Motif analysis of the ChIP-seq data. d N2AFOXF1 and N2Aempty cells were treated with DOX for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis of the indicated sites using an anti-Flag antibody. e N2A-FOXK1KO cells were transfected with pFOXK1 for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis as in ( d ). f Neuro-2a cells were transfected with 200 ng/mL of the indicated plasmids for 24 h before infection and virus titration. The P value represents the difference between each gene under the horizontal line and the control. g The crystal structure of the FOXC2 DBD with DNA was visualized using PyMOL software (PDB ID: 6AKO), with key interactions highlighted. h – j Transfection-infection experiments in Neuro-2a ( h , i ) or N2A-FOXK1KO cells ( j ) performed as in ( f ). k ChIP-qPCR analysis performed as in ( d ). All infections used ICP0-null HSV-1. Cells were infected (MOI = 0.2) for 48 h for ( f , h , i , and j ). n = 2 ( b , c ), 3 ( a , d , e , f , h , i , k ) or 4 ( j ) biologically independent samples. Data were analyzed by one-way ANOVA with Dunnett’s multiple comparisons tests ( a , f , h , i , j ) or two-way ANOVA with Sidak’s multiple comparisons tests ( d , e , k ) and are presented as mean ± SD. Source data are provided as a Source Data file.

    Techniques Used: Infection, ChIP-qPCR, Control, Transfection, ChIP-sequencing, Sequencing, Virus, Titration, Software



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    a 293T cells were infected with WT or ICP0-null HSV-1 (MOI = 10) for 5 h before ChIP-qPCR analysis using an FOXF1 or FOXP1 antibody or an IgG control. b Neuro-2a cells were transfected with pFOXF1 (Flag-tagged) for 42 h, then infected (MOI = 5) for 5 h <t>before</t> <t>ChIP-seq</t> analysis using an anti-Flag antibody. Shown are coverage plots for reads aligned to the HSV-1 genome with terminal repeat regions deleted. Orange vertical sticks represent peaks. Green vertical sticks represent positions of RTAAACA or its complementary <t>sequence.</t> c Upper: the percentages of viral reads relative to total reads in the ChIP-seq data. Lower: Motif analysis of the ChIP-seq data. d N2AFOXF1 and N2Aempty cells were treated with DOX for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis of the indicated sites using an anti-Flag antibody. e N2A-FOXK1KO cells were transfected with pFOXK1 for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis as in ( d ). f Neuro-2a cells were transfected with 200 ng/mL of the indicated plasmids for 24 h before infection and virus titration. The P value represents the difference between each gene under the horizontal line and the control. g The crystal structure of the FOXC2 DBD with DNA was visualized using PyMOL software (PDB ID: 6AKO), with key interactions highlighted. h – j Transfection-infection experiments in Neuro-2a ( h , i ) or N2A-FOXK1KO cells ( j ) performed as in ( f ). k ChIP-qPCR analysis performed as in ( d ). All infections used ICP0-null HSV-1. Cells were infected (MOI = 0.2) for 48 h for ( f , h , i , and j ). n = 2 ( b , c ), 3 ( a , d , e , f , h , i , k ) or 4 ( j ) biologically independent samples. Data were analyzed by one-way ANOVA with Dunnett’s multiple comparisons tests ( a , f , h , i , j ) or two-way ANOVA with Sidak’s multiple comparisons tests ( d , e , k ) and are presented as mean ± SD. Source data are provided as a Source Data file.
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    a 293T cells were infected with WT or ICP0-null HSV-1 (MOI = 10) for 5 h before ChIP-qPCR analysis using an FOXF1 or FOXP1 antibody or an IgG control. b Neuro-2a cells were transfected with pFOXF1 (Flag-tagged) for 42 h, then infected (MOI = 5) for 5 h before ChIP-seq analysis using an anti-Flag antibody. Shown are coverage plots for reads aligned to the HSV-1 genome with terminal repeat regions deleted. Orange vertical sticks represent peaks. Green vertical sticks represent positions of RTAAACA or its complementary sequence. c Upper: the percentages of viral reads relative to total reads in the ChIP-seq data. Lower: Motif analysis of the ChIP-seq data. d N2AFOXF1 and N2Aempty cells were treated with DOX for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis of the indicated sites using an anti-Flag antibody. e N2A-FOXK1KO cells were transfected with pFOXK1 for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis as in ( d ). f Neuro-2a cells were transfected with 200 ng/mL of the indicated plasmids for 24 h before infection and virus titration. The P value represents the difference between each gene under the horizontal line and the control. g The crystal structure of the FOXC2 DBD with DNA was visualized using PyMOL software (PDB ID: 6AKO), with key interactions highlighted. h – j Transfection-infection experiments in Neuro-2a ( h , i ) or N2A-FOXK1KO cells ( j ) performed as in ( f ). k ChIP-qPCR analysis performed as in ( d ). All infections used ICP0-null HSV-1. Cells were infected (MOI = 0.2) for 48 h for ( f , h , i , and j ). n = 2 ( b , c ), 3 ( a , d , e , f , h , i , k ) or 4 ( j ) biologically independent samples. Data were analyzed by one-way ANOVA with Dunnett’s multiple comparisons tests ( a , f , h , i , j ) or two-way ANOVA with Sidak’s multiple comparisons tests ( d , e , k ) and are presented as mean ± SD. Source data are provided as a Source Data file.

    Journal: Nature Communications

    Article Title: Counteracting FOX proteins epigenetically control the herpesvirus lytic-latent balance

    doi: 10.1038/s41467-026-68915-1

    Figure Lengend Snippet: a 293T cells were infected with WT or ICP0-null HSV-1 (MOI = 10) for 5 h before ChIP-qPCR analysis using an FOXF1 or FOXP1 antibody or an IgG control. b Neuro-2a cells were transfected with pFOXF1 (Flag-tagged) for 42 h, then infected (MOI = 5) for 5 h before ChIP-seq analysis using an anti-Flag antibody. Shown are coverage plots for reads aligned to the HSV-1 genome with terminal repeat regions deleted. Orange vertical sticks represent peaks. Green vertical sticks represent positions of RTAAACA or its complementary sequence. c Upper: the percentages of viral reads relative to total reads in the ChIP-seq data. Lower: Motif analysis of the ChIP-seq data. d N2AFOXF1 and N2Aempty cells were treated with DOX for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis of the indicated sites using an anti-Flag antibody. e N2A-FOXK1KO cells were transfected with pFOXK1 for 42 h, then infected (MOI = 5) for 5 h before ChIP-qPCR analysis as in ( d ). f Neuro-2a cells were transfected with 200 ng/mL of the indicated plasmids for 24 h before infection and virus titration. The P value represents the difference between each gene under the horizontal line and the control. g The crystal structure of the FOXC2 DBD with DNA was visualized using PyMOL software (PDB ID: 6AKO), with key interactions highlighted. h – j Transfection-infection experiments in Neuro-2a ( h , i ) or N2A-FOXK1KO cells ( j ) performed as in ( f ). k ChIP-qPCR analysis performed as in ( d ). All infections used ICP0-null HSV-1. Cells were infected (MOI = 0.2) for 48 h for ( f , h , i , and j ). n = 2 ( b , c ), 3 ( a , d , e , f , h , i , k ) or 4 ( j ) biologically independent samples. Data were analyzed by one-way ANOVA with Dunnett’s multiple comparisons tests ( a , f , h , i , j ) or two-way ANOVA with Sidak’s multiple comparisons tests ( d , e , k ) and are presented as mean ± SD. Source data are provided as a Source Data file.

    Article Snippet: The purified input and immunoprecipitated DNA samples were submitted to Novogene for ChIP-seq high-throughput sequencing, followed by data analysis using protocols described previously .

    Techniques: Infection, ChIP-qPCR, Control, Transfection, ChIP-sequencing, Sequencing, Virus, Titration, Software