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  • 96
    ATCC huh7 cells
    ERRγ increases TFR2 mRNA and protein levels. ( A – C ) Q-PCR analysis showing ERRγ, TFR1, and TFR2 mRNA levels. HepG2 cells were transfected with vectors expressing ERRα ( A ), ERRβ ( B ), and ERRγ ( C ) for 48 h. ( D ) Q-PCR analysis showing ERRγ, TFR1, and TFR2 mRNA levels. AML12 cells were transfected with vector expressing ERRγ for 48 h. ( E ) Q-PCR analysis showing TFR2 mRNA levels. HepG2 cells and AML12 cells were treated with GSK4716 (10 μM) for 12 h. ( F ) Q-PCR analysis showing ERRγ and TFR2 mRNA levels in the liver. Ad-GFP and Ad-ERRγ were injected via tail veins into male C57BL/6J mice ( n = 3 per group). Mice were then sacrificed at day 6. ( G , H ) Western blot analysis ( G ) and graphical representation ( H ) showing TFR2 protein levels. <t>Huh7</t> cells were transfected with vector expressing ERRγ (+: 1 μg, ++: 3 μg) for 48 h. ( I , J ) Western blot analysis ( I ) and graphical representation ( J ) showing TFR2 protein levels. AML12 cells were transfected with a vector expressing ERRγ (+: 3 μg) for 48 h. Experiments were performed in duplicate ( G – J ) or triplicate ( A – F ) and repeated at least twice. Error bars show ± SD. * p
    Huh7 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/huh7 cells/product/ATCC
    Average 96 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    huh7 cells - by Bioz Stars, 2022-10
    96/100 stars
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    95
    Thermo Fisher huh7 cells
    Analysis of methods to detect peak changes disproportional to gene expression changes. ( a ) A comparison of Poisson (above) and negative binomial (below) models for read counts under peaks. The negative binomial mean log likelihood of the sample data fell within the 74th and 89st percentiles of 500 simulations for mouse cortex and <t>Huh7</t> cell data, respectively, while the Poisson model failed to capture the sample distributions. ( b ) The percent of sites below an unadjusted p-value threshold of 0.05 for different methods (described in Table 1 ) to detect differential methylation in negative controls between two groups at baseline conditions and positive controls in which methylation processes were disrupted with respect to baseline conditions (Supplementary Table 3 ). The line at 5% indicates the expected proportion of sites given a uniform p-value distribution (see Supplementary Fig. 5c ), while colours indicate negative (orange) and positive (purple) control experiments. ( c ) The correlation between change in gene expression and change in peak expression between conditions for sites identified as differentially methylated in the eight positive control experiments. Pearson’s R = 0.22, 0.10, 0.55, and 0.14 for edgeR, DESeq2, MeTDiff, and QNB, respectively, with p = 0.05, 0.09, 5.8E-87, and 2.4E-11. ( d ) Coverage plots showing changes in peak expression are proportional to changes in gene expression for genes identified as differentially methylated by Bertero et al . (2018) using MeTDiff with activin signaling and an activin-NODAL inhibitor, SB431542 (SB). Lines show the mean coverage across three replicates, while shading shows the standard deviation. Peaks detected as significantly changed are highlighted in yellow. Coding sequences are shown in grey. ( e ) The intersect and union of peaks with p
    Huh7 Cells, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/huh7 cells/product/Thermo Fisher
    Average 95 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    huh7 cells - by Bioz Stars, 2022-10
    95/100 stars
      Buy from Supplier

    Image Search Results


    ERRγ increases TFR2 mRNA and protein levels. ( A – C ) Q-PCR analysis showing ERRγ, TFR1, and TFR2 mRNA levels. HepG2 cells were transfected with vectors expressing ERRα ( A ), ERRβ ( B ), and ERRγ ( C ) for 48 h. ( D ) Q-PCR analysis showing ERRγ, TFR1, and TFR2 mRNA levels. AML12 cells were transfected with vector expressing ERRγ for 48 h. ( E ) Q-PCR analysis showing TFR2 mRNA levels. HepG2 cells and AML12 cells were treated with GSK4716 (10 μM) for 12 h. ( F ) Q-PCR analysis showing ERRγ and TFR2 mRNA levels in the liver. Ad-GFP and Ad-ERRγ were injected via tail veins into male C57BL/6J mice ( n = 3 per group). Mice were then sacrificed at day 6. ( G , H ) Western blot analysis ( G ) and graphical representation ( H ) showing TFR2 protein levels. Huh7 cells were transfected with vector expressing ERRγ (+: 1 μg, ++: 3 μg) for 48 h. ( I , J ) Western blot analysis ( I ) and graphical representation ( J ) showing TFR2 protein levels. AML12 cells were transfected with a vector expressing ERRγ (+: 3 μg) for 48 h. Experiments were performed in duplicate ( G – J ) or triplicate ( A – F ) and repeated at least twice. Error bars show ± SD. * p

    Journal: International Journal of Molecular Sciences

    Article Title: Orphan Nuclear Receptor ERRγ Is a Transcriptional Regulator of CB1 Receptor-Mediated TFR2 Gene Expression in Hepatocytes

    doi: 10.3390/ijms22116021

    Figure Lengend Snippet: ERRγ increases TFR2 mRNA and protein levels. ( A – C ) Q-PCR analysis showing ERRγ, TFR1, and TFR2 mRNA levels. HepG2 cells were transfected with vectors expressing ERRα ( A ), ERRβ ( B ), and ERRγ ( C ) for 48 h. ( D ) Q-PCR analysis showing ERRγ, TFR1, and TFR2 mRNA levels. AML12 cells were transfected with vector expressing ERRγ for 48 h. ( E ) Q-PCR analysis showing TFR2 mRNA levels. HepG2 cells and AML12 cells were treated with GSK4716 (10 μM) for 12 h. ( F ) Q-PCR analysis showing ERRγ and TFR2 mRNA levels in the liver. Ad-GFP and Ad-ERRγ were injected via tail veins into male C57BL/6J mice ( n = 3 per group). Mice were then sacrificed at day 6. ( G , H ) Western blot analysis ( G ) and graphical representation ( H ) showing TFR2 protein levels. Huh7 cells were transfected with vector expressing ERRγ (+: 1 μg, ++: 3 μg) for 48 h. ( I , J ) Western blot analysis ( I ) and graphical representation ( J ) showing TFR2 protein levels. AML12 cells were transfected with a vector expressing ERRγ (+: 3 μg) for 48 h. Experiments were performed in duplicate ( G – J ) or triplicate ( A – F ) and repeated at least twice. Error bars show ± SD. * p

    Article Snippet: Cell Culture, Transfection and Luciferase Assay HepG2 (human liver cancer cell line; ATCC, Manassas, VA, USA) cells and Huh7 (human hepatoma cell line, ATCC) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, high glucose, Welgene, Gyeongsangbuk-do, Korea) and RPMI 1640 medium (Welgene) supplemented with 10% fetal bovine serum and 1% antibiotics (penicillin-streptomycin).

    Techniques: Polymerase Chain Reaction, Transfection, Expressing, Plasmid Preparation, Injection, Mouse Assay, Western Blot

    CB1 receptor signaling induces ERRγ and TFR2 protein expression. ( A – D ) Western blot analysis ( A , C ) and graphical representation ( B , D ) showing ERRγ and TFR2 protein levels. Huh7 cells ( A ) and AML12 cells ( C ) were treated with ACEA (10 μM) for 12 h. ( E – H ) Western blot analysis ( E , G ) and graphical representation ( F , H ) showing ERRγ and TFR2 protein levels. Huh7 cells ( E ) and AML12 cells ( G ) were treated with 2-AG (10 μM) for 12 h. The independent experiments were repeated at least twice. Error bars show ± SD. * p

    Journal: International Journal of Molecular Sciences

    Article Title: Orphan Nuclear Receptor ERRγ Is a Transcriptional Regulator of CB1 Receptor-Mediated TFR2 Gene Expression in Hepatocytes

    doi: 10.3390/ijms22116021

    Figure Lengend Snippet: CB1 receptor signaling induces ERRγ and TFR2 protein expression. ( A – D ) Western blot analysis ( A , C ) and graphical representation ( B , D ) showing ERRγ and TFR2 protein levels. Huh7 cells ( A ) and AML12 cells ( C ) were treated with ACEA (10 μM) for 12 h. ( E – H ) Western blot analysis ( E , G ) and graphical representation ( F , H ) showing ERRγ and TFR2 protein levels. Huh7 cells ( E ) and AML12 cells ( G ) were treated with 2-AG (10 μM) for 12 h. The independent experiments were repeated at least twice. Error bars show ± SD. * p

    Article Snippet: Cell Culture, Transfection and Luciferase Assay HepG2 (human liver cancer cell line; ATCC, Manassas, VA, USA) cells and Huh7 (human hepatoma cell line, ATCC) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, high glucose, Welgene, Gyeongsangbuk-do, Korea) and RPMI 1640 medium (Welgene) supplemented with 10% fetal bovine serum and 1% antibiotics (penicillin-streptomycin).

    Techniques: Expressing, Western Blot

    Analysis of methods to detect peak changes disproportional to gene expression changes. ( a ) A comparison of Poisson (above) and negative binomial (below) models for read counts under peaks. The negative binomial mean log likelihood of the sample data fell within the 74th and 89st percentiles of 500 simulations for mouse cortex and Huh7 cell data, respectively, while the Poisson model failed to capture the sample distributions. ( b ) The percent of sites below an unadjusted p-value threshold of 0.05 for different methods (described in Table 1 ) to detect differential methylation in negative controls between two groups at baseline conditions and positive controls in which methylation processes were disrupted with respect to baseline conditions (Supplementary Table 3 ). The line at 5% indicates the expected proportion of sites given a uniform p-value distribution (see Supplementary Fig. 5c ), while colours indicate negative (orange) and positive (purple) control experiments. ( c ) The correlation between change in gene expression and change in peak expression between conditions for sites identified as differentially methylated in the eight positive control experiments. Pearson’s R = 0.22, 0.10, 0.55, and 0.14 for edgeR, DESeq2, MeTDiff, and QNB, respectively, with p = 0.05, 0.09, 5.8E-87, and 2.4E-11. ( d ) Coverage plots showing changes in peak expression are proportional to changes in gene expression for genes identified as differentially methylated by Bertero et al . (2018) using MeTDiff with activin signaling and an activin-NODAL inhibitor, SB431542 (SB). Lines show the mean coverage across three replicates, while shading shows the standard deviation. Peaks detected as significantly changed are highlighted in yellow. Coding sequences are shown in grey. ( e ) The intersect and union of peaks with p

    Journal: Scientific Reports

    Article Title: Limits in the detection of m6A changes using MeRIP/m6A-seq

    doi: 10.1038/s41598-020-63355-3

    Figure Lengend Snippet: Analysis of methods to detect peak changes disproportional to gene expression changes. ( a ) A comparison of Poisson (above) and negative binomial (below) models for read counts under peaks. The negative binomial mean log likelihood of the sample data fell within the 74th and 89st percentiles of 500 simulations for mouse cortex and Huh7 cell data, respectively, while the Poisson model failed to capture the sample distributions. ( b ) The percent of sites below an unadjusted p-value threshold of 0.05 for different methods (described in Table 1 ) to detect differential methylation in negative controls between two groups at baseline conditions and positive controls in which methylation processes were disrupted with respect to baseline conditions (Supplementary Table 3 ). The line at 5% indicates the expected proportion of sites given a uniform p-value distribution (see Supplementary Fig. 5c ), while colours indicate negative (orange) and positive (purple) control experiments. ( c ) The correlation between change in gene expression and change in peak expression between conditions for sites identified as differentially methylated in the eight positive control experiments. Pearson’s R = 0.22, 0.10, 0.55, and 0.14 for edgeR, DESeq2, MeTDiff, and QNB, respectively, with p = 0.05, 0.09, 5.8E-87, and 2.4E-11. ( d ) Coverage plots showing changes in peak expression are proportional to changes in gene expression for genes identified as differentially methylated by Bertero et al . (2018) using MeTDiff with activin signaling and an activin-NODAL inhibitor, SB431542 (SB). Lines show the mean coverage across three replicates, while shading shows the standard deviation. Peaks detected as significantly changed are highlighted in yellow. Coding sequences are shown in grey. ( e ) The intersect and union of peaks with p

    Article Snippet: Mixed RNA standards were added to 30 μg total RNA from Huh7 cells, along with 0.1 fmol of positive (m6 A-modified Gaussia luciferase RNA, “GLuc”) and negative control (unmodified Cypridina luciferase, “CLuc”) spike-in RNA provided with the N6-methyladenosine Enrichment kit (EpiMark).

    Techniques: Expressing, Methylation, Positive Control, Standard Deviation

    MeRIP-RT-qPCR validation and replicates necessary for the detection of peak changes. ( a ) Relative enrichment of the indicated amounts of an in vitro transcribed standard containing unmodified A or m6A, as measured by MeRIP-RT-qPCR. Data are shown for two independent replicates of three technical replicates each as IP enrichment over input relative to pulldown of a positive control spike-in, with the 0.1 fmol (0.01 m6A: 0.09 A) sample normalized to 1. Bars represent mean ± SEM of two independent replicates. ***p ≤ 0.005 by unpaired Student’s t-test. b - d ) Linear regression of relative m6A enrichment from ( a ). Points and error bars mark mean ± SEM of two independent replicates. ( c ) Change in MeRIP-RT-qPCR vs. MeRIP-seq enrichment for peaks detected as significantly differentially expressed with infection of Huh7 cells by dengue virus, Zika virus, and hepatitis C virus. ( d ) Number of replicates of infected vs. uninfected cells needed to detect the peaks in ( c ). Replicates were randomly subsampled 10 times to calculate the fraction of subsamples in which peaks were called as significant by the GLMs or QNB. Boxes span the 1st to 3rd quartiles, with medians indicated. Whiskers show the minimum and maximum points within ±1.5x the interquartile distance from the boxes. Results for each subsample of replicates are shown as jittered points.

    Journal: Scientific Reports

    Article Title: Limits in the detection of m6A changes using MeRIP/m6A-seq

    doi: 10.1038/s41598-020-63355-3

    Figure Lengend Snippet: MeRIP-RT-qPCR validation and replicates necessary for the detection of peak changes. ( a ) Relative enrichment of the indicated amounts of an in vitro transcribed standard containing unmodified A or m6A, as measured by MeRIP-RT-qPCR. Data are shown for two independent replicates of three technical replicates each as IP enrichment over input relative to pulldown of a positive control spike-in, with the 0.1 fmol (0.01 m6A: 0.09 A) sample normalized to 1. Bars represent mean ± SEM of two independent replicates. ***p ≤ 0.005 by unpaired Student’s t-test. b - d ) Linear regression of relative m6A enrichment from ( a ). Points and error bars mark mean ± SEM of two independent replicates. ( c ) Change in MeRIP-RT-qPCR vs. MeRIP-seq enrichment for peaks detected as significantly differentially expressed with infection of Huh7 cells by dengue virus, Zika virus, and hepatitis C virus. ( d ) Number of replicates of infected vs. uninfected cells needed to detect the peaks in ( c ). Replicates were randomly subsampled 10 times to calculate the fraction of subsamples in which peaks were called as significant by the GLMs or QNB. Boxes span the 1st to 3rd quartiles, with medians indicated. Whiskers show the minimum and maximum points within ±1.5x the interquartile distance from the boxes. Results for each subsample of replicates are shown as jittered points.

    Article Snippet: Mixed RNA standards were added to 30 μg total RNA from Huh7 cells, along with 0.1 fmol of positive (m6 A-modified Gaussia luciferase RNA, “GLuc”) and negative control (unmodified Cypridina luciferase, “CLuc”) spike-in RNA provided with the N6-methyladenosine Enrichment kit (EpiMark).

    Techniques: Quantitative RT-PCR, In Vitro, Positive Control, Infection

    Thresholds for peak detection. ( a ) m6A(m) site detection in MeRIP-seq data from mouse cortex (left) and human liver cells (Huh7, right) shows saturation of peak detection as transcript coverage approaches 10–50X for replicates at basal conditions, with peaks merged from all replicates. ( b ) The total number of peaks captured increases with more replicates, with single replicates capturing a median of 66–78% of total peaks depending on study. Boxes span the 1st to 3rd quartiles of distributions for random subsamples of replicates, with lines indicating the median number of peaks, and whiskers showing the minimum and maximum points within ±1.5x the interquartile distance from the boxes. Jittered points show results for each random subsample (a total of 6 subsamples per replicate number for the mouse cortex data and 12 for the Huh7 data). ( c ) The percent of peaks detected in at least r replicates for the same data sets.

    Journal: Scientific Reports

    Article Title: Limits in the detection of m6A changes using MeRIP/m6A-seq

    doi: 10.1038/s41598-020-63355-3

    Figure Lengend Snippet: Thresholds for peak detection. ( a ) m6A(m) site detection in MeRIP-seq data from mouse cortex (left) and human liver cells (Huh7, right) shows saturation of peak detection as transcript coverage approaches 10–50X for replicates at basal conditions, with peaks merged from all replicates. ( b ) The total number of peaks captured increases with more replicates, with single replicates capturing a median of 66–78% of total peaks depending on study. Boxes span the 1st to 3rd quartiles of distributions for random subsamples of replicates, with lines indicating the median number of peaks, and whiskers showing the minimum and maximum points within ±1.5x the interquartile distance from the boxes. Jittered points show results for each random subsample (a total of 6 subsamples per replicate number for the mouse cortex data and 12 for the Huh7 data). ( c ) The percent of peaks detected in at least r replicates for the same data sets.

    Article Snippet: Mixed RNA standards were added to 30 μg total RNA from Huh7 cells, along with 0.1 fmol of positive (m6 A-modified Gaussia luciferase RNA, “GLuc”) and negative control (unmodified Cypridina luciferase, “CLuc”) spike-in RNA provided with the N6-methyladenosine Enrichment kit (EpiMark).

    Techniques: