fam dye labeled probes  (Thermo Fisher)


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    Structured Review

    Thermo Fisher fam dye labeled probes
    Fam Dye Labeled Probes, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fam dye labeled probes/product/Thermo Fisher
    Average 85 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    fam dye labeled probes - by Bioz Stars, 2020-08
    85/100 stars

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    Related Articles

    Polymerase Chain Reaction:

    Article Title: Exogenous Fibroblast Growth Factor-10 Induces Cystic Lung Development with Altered Target Gene Expression in the Presence of Heparin in Cultures of Embryonic Rat Lung
    Article Snippet: .. PCR primers, FAM dye-labeled probes and Taqman Universal PCR master mix were obtained from Applied Biosystems. .. Rat lung cDNA was synthesized from RNA as described earlier [ ].

    Article Title: Hapten Application to the Skin Induces an Inflammatory Program Directing Hapten-Primed Effector CD8 T Cell Interaction With Hapten-Presenting Endothelial Cells
    Article Snippet: .. PCR was performed using custom primers and FAM dye-labeled probes (Applied Biosystems) for mouse IFN-γ, IL-17, CXCL1, TNFα, ICAM-1, and Mrpl 32 (gene assay ID#: Mm00801778_m1, Mm00439619_m1, Mm00433859_m1, Mm00443258_m1, Mm00516023_m1 and, Mm00777741_sH respectively). .. The comparative CT method for relative quantitation of cytokine gene expression was used where log measurements for each sample are made during amplification and the expression level of the Mrpl 32 housekeeping gene is subtracted from the expression level for each test cytokine gene.

    Article Title: CD8 T CELLS PRODUCING IL-17 AND IFN-γ INITIATE THE INNATE IMMUNE RESPONSE REQUIRED FOR RESPONSES TO ANTIGEN SKIN CHALLENGE
    Article Snippet: .. PCR was performed using custom primers and FAM dye-labeled probes (Applied Biosystems) for mouse TNFα, IFN-γ, IL-17, CXCL1/, CXCL2, IL-10, IL-21, and Mrpl 32 (gene assay ID#: Mm00443258_m1, Mm00801778_m1, Mm00439619_m1, Mm00433859_m1, Mm00436450_m1, Mm00439616_m1, Mm00517640_m1, and, Mm00777741_sH, respectively). .. The comparative CT method for relative quantitation of cytokine gene expression was used where log measurements for each sample are made during amplification and the expression level of the Mrpl 32 housekeeping gene is subtracted from the expression level for each test cytokine gene.

    Article Title: Neutrophil Expression of FasL and Perforin Directs Effector CD8 T Cell Infiltration into Antigen Challenged Skin
    Article Snippet: .. PCR was performed using custom primers and FAM dye-labeled probes (Applied Biosystems, Foster City, CA) for mouse FasL, perforin, IL-17, IFN-γ, CXCL9, CXCL10, CCL1, CCL2, CCL5, and Mrpl 32 (gene assay ID#: Mm00438864_m1, Mm00812512_m1, Mm00439619_m1, Mm00801778_m1, Mm00434946_m1, Mm00445235_m1, Mm00441236_m1, Mm00441242_m1, Mm01302428_m1, and Mm00777741_sH respectively). .. The QT of gene expression of one sample, the RNA isolated from the skin homogenate of naïve, not challenged wild-type mice, was arbitrarily set at 1.0 and used to determine the expression levels of the remaining samples.

    Article Title: IL-1 Receptor Signaling Is Required at Multiple Stages of Sensitization and Elicitation of the Contact Hypersensitivity Response
    Article Snippet: .. PCR was performed using custom primers and FAM dye-labeled probes (Applied Biosystems, Foster City, CA) for mouse CXCL1, IFN-γ, IL-17, TNF-α ICAM-1, CCL19, CCL21, and Mrpl 32 (gene assay ID#: Mm00433859_m1, Mm00801778_m1, Mm00439619_m1, Mm00443258_m1, Mm00516023_m1 Mm00434165_m1, Mm03646971_gH, and, Mm00777741_sH respectively). .. The comparative CT method for relative quantitation of cytokine gene expression was used where log measurements for each sample are made during amplification and the expression level of the Mrpl 32 housekeeping gene is subtracted from the expression level for each test cytokine gene.

    Gene Assay:

    Article Title: Hapten Application to the Skin Induces an Inflammatory Program Directing Hapten-Primed Effector CD8 T Cell Interaction With Hapten-Presenting Endothelial Cells
    Article Snippet: .. PCR was performed using custom primers and FAM dye-labeled probes (Applied Biosystems) for mouse IFN-γ, IL-17, CXCL1, TNFα, ICAM-1, and Mrpl 32 (gene assay ID#: Mm00801778_m1, Mm00439619_m1, Mm00433859_m1, Mm00443258_m1, Mm00516023_m1 and, Mm00777741_sH respectively). .. The comparative CT method for relative quantitation of cytokine gene expression was used where log measurements for each sample are made during amplification and the expression level of the Mrpl 32 housekeeping gene is subtracted from the expression level for each test cytokine gene.

    Article Title: CD8 T CELLS PRODUCING IL-17 AND IFN-γ INITIATE THE INNATE IMMUNE RESPONSE REQUIRED FOR RESPONSES TO ANTIGEN SKIN CHALLENGE
    Article Snippet: .. PCR was performed using custom primers and FAM dye-labeled probes (Applied Biosystems) for mouse TNFα, IFN-γ, IL-17, CXCL1/, CXCL2, IL-10, IL-21, and Mrpl 32 (gene assay ID#: Mm00443258_m1, Mm00801778_m1, Mm00439619_m1, Mm00433859_m1, Mm00436450_m1, Mm00439616_m1, Mm00517640_m1, and, Mm00777741_sH, respectively). .. The comparative CT method for relative quantitation of cytokine gene expression was used where log measurements for each sample are made during amplification and the expression level of the Mrpl 32 housekeeping gene is subtracted from the expression level for each test cytokine gene.

    Article Title: Neutrophil Expression of FasL and Perforin Directs Effector CD8 T Cell Infiltration into Antigen Challenged Skin
    Article Snippet: .. PCR was performed using custom primers and FAM dye-labeled probes (Applied Biosystems, Foster City, CA) for mouse FasL, perforin, IL-17, IFN-γ, CXCL9, CXCL10, CCL1, CCL2, CCL5, and Mrpl 32 (gene assay ID#: Mm00438864_m1, Mm00812512_m1, Mm00439619_m1, Mm00801778_m1, Mm00434946_m1, Mm00445235_m1, Mm00441236_m1, Mm00441242_m1, Mm01302428_m1, and Mm00777741_sH respectively). .. The QT of gene expression of one sample, the RNA isolated from the skin homogenate of naïve, not challenged wild-type mice, was arbitrarily set at 1.0 and used to determine the expression levels of the remaining samples.

    Article Title: IL-1 Receptor Signaling Is Required at Multiple Stages of Sensitization and Elicitation of the Contact Hypersensitivity Response
    Article Snippet: .. PCR was performed using custom primers and FAM dye-labeled probes (Applied Biosystems, Foster City, CA) for mouse CXCL1, IFN-γ, IL-17, TNF-α ICAM-1, CCL19, CCL21, and Mrpl 32 (gene assay ID#: Mm00433859_m1, Mm00801778_m1, Mm00439619_m1, Mm00443258_m1, Mm00516023_m1 Mm00434165_m1, Mm03646971_gH, and, Mm00777741_sH respectively). .. The comparative CT method for relative quantitation of cytokine gene expression was used where log measurements for each sample are made during amplification and the expression level of the Mrpl 32 housekeeping gene is subtracted from the expression level for each test cytokine gene.

    Generated:

    Article Title: Analysis of a Genome-Wide Association Study-Linked Locus (CCR6) in Asian Rheumatoid Arthritis
    Article Snippet: .. Fluorescent signals of VIC® dye-labeled and FAM™ dye-labeled probes were analyzed at end-point; allele call and genotype were generated automatically on Applied Biosystems 7500 Real-Time PCR System. ..

    Real-time Polymerase Chain Reaction:

    Article Title: Analysis of a Genome-Wide Association Study-Linked Locus (CCR6) in Asian Rheumatoid Arthritis
    Article Snippet: .. Fluorescent signals of VIC® dye-labeled and FAM™ dye-labeled probes were analyzed at end-point; allele call and genotype were generated automatically on Applied Biosystems 7500 Real-Time PCR System. ..

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  • 99
    Thermo Fisher gene exp myc hs00153408 m1
    ERK inhibition and KRAS silencing impairs mitochondrial function in PDAC cells. a , Cells were treated with vehicle (DMSO) or SCH772984 (ERKi, 1 μM) for 24 h. Shown is quantification of mean fluorescence of MitoTracker green staining, normalized to DMSO for each cell line across three independent experiments. P values are from two-sided, unpaired t -test; error bars denote s.e.m. b , Mitochondrial morphologies of PDAC cells treated with SCH772984 (ERKi, 1 µM) for 24 h. Green, anti-TOMM20; blue, DAPI. Scale bar, 20 μm. c , Quantitation of mitochondrial morphologies observed in cells shown in b . Some 50 cells per condition per repetition were blindly scored and data are averages of four independent experiments; error bars denote s.e.m. d , Pa14C cells were treated with SCH772984 (ERKi, 1 µM) for 1 h. Immunoblot of phosphorylated DRP1 (S616) (pDRP1), total DRP1 and β-actin is representative of three independent experiments. e , Mitochondrial morphologies of PDAC cells treated with SCH772984 (ERKi, 1 µM) for 24 h. Green, Anti-TOMM20; blue, DAPI; scale bar, 20 μm. f , Quantitation of mitochondrial morphologies observed in cells shown in e . Some 50 cells per condition per repetition were blindly scored; data are means of four independent experiments; error bars denote s.e.m. g , PDAC cells were treated with SCH772984 (ERKi, 1 μM) for 24 h. Immunoblot of pDRP1, total DRP1, <t>MYC,</t> phosphorylated RSK (pRSK) and β-actin is representative of three independent experiments. h , Cell lines derived from the iKRAS PDAC mouse model were deprived of doxycycline (Dox) to turn off Kras G12D for 24 h. Representative transmission electron microscopy (TEM) micrographs displaying mitochondrial morphologies in the presence and absence of doxycycline; images are representative of six independent experiments; scale bar, 500 nm. i , Cells were treated as described in a . Quantification of relative mitochondrial potential via labeling with the JC-1 mitochondrial dye. Data are the mean of three independent experiments; P values are from two-sided, unpaired t -test; error bars denote s.d. of median ratios of JC-1 aggregate fluorescence to JC-1 monomer fluorescence. j , Representative histograms from Pa01C and Pa14C cells quantified in i ; as a control, the uncoupler CCCP was added to acquired DMSO samples to establish minimum potential. k , OCR response of PDAC cells treated with DMSO or SCH772984 (ERKi, 1 μM) for 1.5 h; shown is mean OCR of three independent experiments; error bars denote s.e.m. of mean OCR across replicates. l , OCR response of PDAC cells treated with DMSO or SCH772984 (ERKi, 1 μM) for 24 h. Data for HPAC and Pa01C lines are the mean of nine independent experiments; data for Pa14C are the mean of eight independent experiments, and data for PANC-1 are the mean of three independent experiments. P values are from two-sided, unpaired t -test, comparing treatment conditions to DMSO, which was normalized to 100 for each measurement; error bars denote s.e.m.
    Gene Exp Myc Hs00153408 M1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 65 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gene exp myc hs00153408 m1/product/Thermo Fisher
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    99
    Thermo Fisher gene exp esr1 hs00174860 m1
    Cells were transiently transfected for 24 h with 3x ERE-luc and phRL-TK Renilla internal control plasmid together with either pDsRed-express-C1 (empty vector control), <t>pDsRed-wt-ESR1</t> or pDsRed-Δ7-ESR1. Following transfection, cells were incubated for 24 h in the absence or presence of the indicated concentrations of 17β-estradiol ( A ) or 50 pM of 17β-estradiol ( B ). Values are mean +SEM averaged from n = 6 replicate cultures and presented as luciferase activity relative to the empty vector construct of the vehicle-treated control condition (*** P
    Gene Exp Esr1 Hs00174860 M1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 36 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gene exp esr1 hs00174860 m1/product/Thermo Fisher
    Average 99 stars, based on 36 article reviews
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    97
    Thermo Fisher fam dye labeled taqman mgb probe
    Cells were transiently transfected for 24 h with 3x ERE-luc and phRL-TK Renilla internal control plasmid together with either pDsRed-express-C1 (empty vector control), <t>pDsRed-wt-ESR1</t> or pDsRed-Δ7-ESR1. Following transfection, cells were incubated for 24 h in the absence or presence of the indicated concentrations of 17β-estradiol ( A ) or 50 pM of 17β-estradiol ( B ). Values are mean +SEM averaged from n = 6 replicate cultures and presented as luciferase activity relative to the empty vector construct of the vehicle-treated control condition (*** P
    Fam Dye Labeled Taqman Mgb Probe, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/fam dye labeled taqman mgb probe/product/Thermo Fisher
    Average 97 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    fam dye labeled taqman mgb probe - by Bioz Stars, 2020-08
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    Image Search Results


    ERK inhibition and KRAS silencing impairs mitochondrial function in PDAC cells. a , Cells were treated with vehicle (DMSO) or SCH772984 (ERKi, 1 μM) for 24 h. Shown is quantification of mean fluorescence of MitoTracker green staining, normalized to DMSO for each cell line across three independent experiments. P values are from two-sided, unpaired t -test; error bars denote s.e.m. b , Mitochondrial morphologies of PDAC cells treated with SCH772984 (ERKi, 1 µM) for 24 h. Green, anti-TOMM20; blue, DAPI. Scale bar, 20 μm. c , Quantitation of mitochondrial morphologies observed in cells shown in b . Some 50 cells per condition per repetition were blindly scored and data are averages of four independent experiments; error bars denote s.e.m. d , Pa14C cells were treated with SCH772984 (ERKi, 1 µM) for 1 h. Immunoblot of phosphorylated DRP1 (S616) (pDRP1), total DRP1 and β-actin is representative of three independent experiments. e , Mitochondrial morphologies of PDAC cells treated with SCH772984 (ERKi, 1 µM) for 24 h. Green, Anti-TOMM20; blue, DAPI; scale bar, 20 μm. f , Quantitation of mitochondrial morphologies observed in cells shown in e . Some 50 cells per condition per repetition were blindly scored; data are means of four independent experiments; error bars denote s.e.m. g , PDAC cells were treated with SCH772984 (ERKi, 1 μM) for 24 h. Immunoblot of pDRP1, total DRP1, MYC, phosphorylated RSK (pRSK) and β-actin is representative of three independent experiments. h , Cell lines derived from the iKRAS PDAC mouse model were deprived of doxycycline (Dox) to turn off Kras G12D for 24 h. Representative transmission electron microscopy (TEM) micrographs displaying mitochondrial morphologies in the presence and absence of doxycycline; images are representative of six independent experiments; scale bar, 500 nm. i , Cells were treated as described in a . Quantification of relative mitochondrial potential via labeling with the JC-1 mitochondrial dye. Data are the mean of three independent experiments; P values are from two-sided, unpaired t -test; error bars denote s.d. of median ratios of JC-1 aggregate fluorescence to JC-1 monomer fluorescence. j , Representative histograms from Pa01C and Pa14C cells quantified in i ; as a control, the uncoupler CCCP was added to acquired DMSO samples to establish minimum potential. k , OCR response of PDAC cells treated with DMSO or SCH772984 (ERKi, 1 μM) for 1.5 h; shown is mean OCR of three independent experiments; error bars denote s.e.m. of mean OCR across replicates. l , OCR response of PDAC cells treated with DMSO or SCH772984 (ERKi, 1 μM) for 24 h. Data for HPAC and Pa01C lines are the mean of nine independent experiments; data for Pa14C are the mean of eight independent experiments, and data for PANC-1 are the mean of three independent experiments. P values are from two-sided, unpaired t -test, comparing treatment conditions to DMSO, which was normalized to 100 for each measurement; error bars denote s.e.m.

    Journal: Nature medicine

    Article Title: Combination of ERK and autophagy inhibition as a treatment approach for pancreatic cancer

    doi: 10.1038/s41591-019-0368-8

    Figure Lengend Snippet: ERK inhibition and KRAS silencing impairs mitochondrial function in PDAC cells. a , Cells were treated with vehicle (DMSO) or SCH772984 (ERKi, 1 μM) for 24 h. Shown is quantification of mean fluorescence of MitoTracker green staining, normalized to DMSO for each cell line across three independent experiments. P values are from two-sided, unpaired t -test; error bars denote s.e.m. b , Mitochondrial morphologies of PDAC cells treated with SCH772984 (ERKi, 1 µM) for 24 h. Green, anti-TOMM20; blue, DAPI. Scale bar, 20 μm. c , Quantitation of mitochondrial morphologies observed in cells shown in b . Some 50 cells per condition per repetition were blindly scored and data are averages of four independent experiments; error bars denote s.e.m. d , Pa14C cells were treated with SCH772984 (ERKi, 1 µM) for 1 h. Immunoblot of phosphorylated DRP1 (S616) (pDRP1), total DRP1 and β-actin is representative of three independent experiments. e , Mitochondrial morphologies of PDAC cells treated with SCH772984 (ERKi, 1 µM) for 24 h. Green, Anti-TOMM20; blue, DAPI; scale bar, 20 μm. f , Quantitation of mitochondrial morphologies observed in cells shown in e . Some 50 cells per condition per repetition were blindly scored; data are means of four independent experiments; error bars denote s.e.m. g , PDAC cells were treated with SCH772984 (ERKi, 1 μM) for 24 h. Immunoblot of pDRP1, total DRP1, MYC, phosphorylated RSK (pRSK) and β-actin is representative of three independent experiments. h , Cell lines derived from the iKRAS PDAC mouse model were deprived of doxycycline (Dox) to turn off Kras G12D for 24 h. Representative transmission electron microscopy (TEM) micrographs displaying mitochondrial morphologies in the presence and absence of doxycycline; images are representative of six independent experiments; scale bar, 500 nm. i , Cells were treated as described in a . Quantification of relative mitochondrial potential via labeling with the JC-1 mitochondrial dye. Data are the mean of three independent experiments; P values are from two-sided, unpaired t -test; error bars denote s.d. of median ratios of JC-1 aggregate fluorescence to JC-1 monomer fluorescence. j , Representative histograms from Pa01C and Pa14C cells quantified in i ; as a control, the uncoupler CCCP was added to acquired DMSO samples to establish minimum potential. k , OCR response of PDAC cells treated with DMSO or SCH772984 (ERKi, 1 μM) for 1.5 h; shown is mean OCR of three independent experiments; error bars denote s.e.m. of mean OCR across replicates. l , OCR response of PDAC cells treated with DMSO or SCH772984 (ERKi, 1 μM) for 24 h. Data for HPAC and Pa01C lines are the mean of nine independent experiments; data for Pa14C are the mean of eight independent experiments, and data for PANC-1 are the mean of three independent experiments. P values are from two-sided, unpaired t -test, comparing treatment conditions to DMSO, which was normalized to 100 for each measurement; error bars denote s.e.m.

    Article Snippet: Real-time quantitative Taqman PCR was performed on the QuantStudio 6 Flex (Thermo Fisher) with minor groove binder FAM dye-labeled probes against MYC (Hs00153408_m1, Thermo Fisher), SQSTM1 (Hs1061917_g1, Thermo Fisher), GABARAPL1 (Hs00740588_mH, Thermo Fisher), WIPI1 (Hs00924447_m1, Thermo Fisher), BECN1 (Hs01007018_m1, Thermo Fisher) and PRKAA1 (Hs01562315_m1, Thermo Fisher) and endogenous control VIC and TAMRA dye-labeled ACTB (Thermo Fisher).

    Techniques: Inhibition, Fluorescence, Staining, Quantitation Assay, Derivative Assay, Transmission Assay, Electron Microscopy, Transmission Electron Microscopy, Labeling

    Cells were transiently transfected for 24 h with 3x ERE-luc and phRL-TK Renilla internal control plasmid together with either pDsRed-express-C1 (empty vector control), pDsRed-wt-ESR1 or pDsRed-Δ7-ESR1. Following transfection, cells were incubated for 24 h in the absence or presence of the indicated concentrations of 17β-estradiol ( A ) or 50 pM of 17β-estradiol ( B ). Values are mean +SEM averaged from n = 6 replicate cultures and presented as luciferase activity relative to the empty vector construct of the vehicle-treated control condition (*** P

    Journal: Human Molecular Genetics

    Article Title: Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia

    doi: 10.1093/hmg/ddn130

    Figure Lengend Snippet: Cells were transiently transfected for 24 h with 3x ERE-luc and phRL-TK Renilla internal control plasmid together with either pDsRed-express-C1 (empty vector control), pDsRed-wt-ESR1 or pDsRed-Δ7-ESR1. Following transfection, cells were incubated for 24 h in the absence or presence of the indicated concentrations of 17β-estradiol ( A ) or 50 pM of 17β-estradiol ( B ). Values are mean +SEM averaged from n = 6 replicate cultures and presented as luciferase activity relative to the empty vector construct of the vehicle-treated control condition (*** P

    Article Snippet: Each qPCR reaction contained 3 µl cDNA template (corresponding to 90 ng cDNA), 5 µl Master Mix (Eurogentec, California), 0.5 µl 20X assay-on demand mix containing forward and reverse primers and FAM™ dye-labeled TaqMan® MGB probe (Hs00174860_m1) and 1.5 µl H2 O.

    Techniques: Transfection, Plasmid Preparation, Incubation, Luciferase, Activity Assay, Construct

    ( A ) The PCR products produced after nested PCR for ESR1 from cDNA derived from the DLPFC of patients with schizophrenia. Note that the samples are migrating on a slight downward diagonal. Lane 1 contains the 100 bp DNA ladder (L). The bright band in the first three sample lanes (lanes 2–4) and the last 2 lanes (15 and 16) corresponds to the expected 1380 bp amplicon (horizontal arrow). This ∼1.4 band would be predicted if all 8 coding exons were present in the ESR1 transcript (wild-type). Many bands with smaller than the predicted sizes are found in the range of 1 to 1.3 kb and can occur in different individuals (for example, compare lanes 4 to lane 5) or within the same individual (lanes 7, 8, 11, 13 and 14). The exact identities of these bands could not be definitively identified at this stage (see Materials and Methods). Note that in lanes 5, 6, 7 and 10 no wild-type bands are detected. In the 12th lane, a larger than predicted amplicon was observed (vertical arrow, 1493 bp). In panel B, the 1493 bp ESR1 transcript was confirmed to be about 100 bp longer by a separate PCR directly targeting ESR1 exons 4 and 5 in normal individuals (N) and in the patient with schizophrenia with this genomic insertion (S).

    Journal: Human Molecular Genetics

    Article Title: Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia

    doi: 10.1093/hmg/ddn130

    Figure Lengend Snippet: ( A ) The PCR products produced after nested PCR for ESR1 from cDNA derived from the DLPFC of patients with schizophrenia. Note that the samples are migrating on a slight downward diagonal. Lane 1 contains the 100 bp DNA ladder (L). The bright band in the first three sample lanes (lanes 2–4) and the last 2 lanes (15 and 16) corresponds to the expected 1380 bp amplicon (horizontal arrow). This ∼1.4 band would be predicted if all 8 coding exons were present in the ESR1 transcript (wild-type). Many bands with smaller than the predicted sizes are found in the range of 1 to 1.3 kb and can occur in different individuals (for example, compare lanes 4 to lane 5) or within the same individual (lanes 7, 8, 11, 13 and 14). The exact identities of these bands could not be definitively identified at this stage (see Materials and Methods). Note that in lanes 5, 6, 7 and 10 no wild-type bands are detected. In the 12th lane, a larger than predicted amplicon was observed (vertical arrow, 1493 bp). In panel B, the 1493 bp ESR1 transcript was confirmed to be about 100 bp longer by a separate PCR directly targeting ESR1 exons 4 and 5 in normal individuals (N) and in the patient with schizophrenia with this genomic insertion (S).

    Article Snippet: Each qPCR reaction contained 3 µl cDNA template (corresponding to 90 ng cDNA), 5 µl Master Mix (Eurogentec, California), 0.5 µl 20X assay-on demand mix containing forward and reverse primers and FAM™ dye-labeled TaqMan® MGB probe (Hs00174860_m1) and 1.5 µl H2 O.

    Techniques: Polymerase Chain Reaction, Produced, Nested PCR, Derivative Assay, Amplification

    A schematic figure shows the general location of ESR1 common SNPs (arrows) used in association analyses. Gray horizontal bars indicate the regions of the ESR1 gene that were re-sequenced. The eight coding exons and the insertion are indicated by thin black vertical lines. ESR1 introns are shown as open horizontal bars (note thy can be grey or white). Numbers at the bottom correspond to exons and letters represent the different alternative start sites of transcription (indicated on gene with flags). Lines connecting exons C and B to exon 1 represent some of the alternative splicing. Other alternative 5′-UTR exons upstream of exon D are not shown.

    Journal: Human Molecular Genetics

    Article Title: Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia

    doi: 10.1093/hmg/ddn130

    Figure Lengend Snippet: A schematic figure shows the general location of ESR1 common SNPs (arrows) used in association analyses. Gray horizontal bars indicate the regions of the ESR1 gene that were re-sequenced. The eight coding exons and the insertion are indicated by thin black vertical lines. ESR1 introns are shown as open horizontal bars (note thy can be grey or white). Numbers at the bottom correspond to exons and letters represent the different alternative start sites of transcription (indicated on gene with flags). Lines connecting exons C and B to exon 1 represent some of the alternative splicing. Other alternative 5′-UTR exons upstream of exon D are not shown.

    Article Snippet: Each qPCR reaction contained 3 µl cDNA template (corresponding to 90 ng cDNA), 5 µl Master Mix (Eurogentec, California), 0.5 µl 20X assay-on demand mix containing forward and reverse primers and FAM™ dye-labeled TaqMan® MGB probe (Hs00174860_m1) and 1.5 µl H2 O.

    Techniques:

    Schematic representations of the variation in transcription factor binding sites (TFBS) for the two promoter haplotypes of ESR1 are diagrammed. The top represents the common haplotype for C4, C5, C10 and C11 (1, 2, 1, 1, 1) that is not associated with the risk for schizophrenia. The bottom schematic shows the haplotype associated with risk (2, 1, 2, 2, 2). Ovals represent transcription factor binding to either the sense (upper) or antisense (lower) ESR1 DNA strand. Note the loss of a predicted biding of a transcription factor sites at C4, C5 and C11 and a gain of transcription factor binding site at C10 and Indel-C1 in the risk haplotype. Black oval, SOX5; grey ovals, MYT1; checkered oval, NGF1C; dotted oval, AP4; hatched oval, RP580 or ZNF238; white oval, myb.

    Journal: Human Molecular Genetics

    Article Title: Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia

    doi: 10.1093/hmg/ddn130

    Figure Lengend Snippet: Schematic representations of the variation in transcription factor binding sites (TFBS) for the two promoter haplotypes of ESR1 are diagrammed. The top represents the common haplotype for C4, C5, C10 and C11 (1, 2, 1, 1, 1) that is not associated with the risk for schizophrenia. The bottom schematic shows the haplotype associated with risk (2, 1, 2, 2, 2). Ovals represent transcription factor binding to either the sense (upper) or antisense (lower) ESR1 DNA strand. Note the loss of a predicted biding of a transcription factor sites at C4, C5 and C11 and a gain of transcription factor binding site at C10 and Indel-C1 in the risk haplotype. Black oval, SOX5; grey ovals, MYT1; checkered oval, NGF1C; dotted oval, AP4; hatched oval, RP580 or ZNF238; white oval, myb.

    Article Snippet: Each qPCR reaction contained 3 µl cDNA template (corresponding to 90 ng cDNA), 5 µl Master Mix (Eurogentec, California), 0.5 µl 20X assay-on demand mix containing forward and reverse primers and FAM™ dye-labeled TaqMan® MGB probe (Hs00174860_m1) and 1.5 µl H2 O.

    Techniques: Binding Assay

    Scatter plot showing the average quantity of ESR1 mRNA levels normalized to the geometric mean of four housekeeper (HSKPs) mRNAs on the Y -axis as determined by real time qPCR. The values of ESR for patients with schizophrenia are plotted according to the PvuII (C11) genotype with C being the risk allele. Those patients homozygous for the risk allele (CC), have significantly lower expression compared to the other genotype groups (T/C and T/T). * P > 0.05.

    Journal: Human Molecular Genetics

    Article Title: Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia

    doi: 10.1093/hmg/ddn130

    Figure Lengend Snippet: Scatter plot showing the average quantity of ESR1 mRNA levels normalized to the geometric mean of four housekeeper (HSKPs) mRNAs on the Y -axis as determined by real time qPCR. The values of ESR for patients with schizophrenia are plotted according to the PvuII (C11) genotype with C being the risk allele. Those patients homozygous for the risk allele (CC), have significantly lower expression compared to the other genotype groups (T/C and T/T). * P > 0.05.

    Article Snippet: Each qPCR reaction contained 3 µl cDNA template (corresponding to 90 ng cDNA), 5 µl Master Mix (Eurogentec, California), 0.5 µl 20X assay-on demand mix containing forward and reverse primers and FAM™ dye-labeled TaqMan® MGB probe (Hs00174860_m1) and 1.5 µl H2 O.

    Techniques: Real-time Polymerase Chain Reaction, Electron Paramagnetic Resonance, Expressing

    Schematic view of the ESR1 transcripts detected from cDNA from the DLPFC of adult humans. Nineteen different exon-deleted ESR1 mRNAs are depicted with the boxes representing the 8 known coding exons according to Genbank entry NM_000125. *the partial exon deletion, N the variant only detected in normal controls, P the variant only detected in psychiatric patients. WT = wild-type ESR1.

    Journal: Human Molecular Genetics

    Article Title: Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia

    doi: 10.1093/hmg/ddn130

    Figure Lengend Snippet: Schematic view of the ESR1 transcripts detected from cDNA from the DLPFC of adult humans. Nineteen different exon-deleted ESR1 mRNAs are depicted with the boxes representing the 8 known coding exons according to Genbank entry NM_000125. *the partial exon deletion, N the variant only detected in normal controls, P the variant only detected in psychiatric patients. WT = wild-type ESR1.

    Article Snippet: Each qPCR reaction contained 3 µl cDNA template (corresponding to 90 ng cDNA), 5 µl Master Mix (Eurogentec, California), 0.5 µl 20X assay-on demand mix containing forward and reverse primers and FAM™ dye-labeled TaqMan® MGB probe (Hs00174860_m1) and 1.5 µl H2 O.

    Techniques: Variant Assay