fam labeled taqman probes  (Thermo Fisher)


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    Name:
    TaqMan Gene Expression Assay FAM
    Description:
    Applied Biosystems TaqMan Gene Expression assays are used for quantitative real time PCR analysis of gene expression and consist of a pair of unlabeled PCR primers and a TaqMan probe with a dye label FAM on the 5 end and a minor groove binder MGB and non fluorescent quencher NFQ on the 3 end Features of TaqMan Gene Expression assays include • Easy to use just add cDNA and master mix and run the qPCR no melt curves required • Specific TaqMan assays use proprietary MGB containing probes that can be up to 15 bases shorter than non MGB probes improving the specificity of the assay • Sensitive TaqMan assays are ideal for measuring low levels of expression or low abundance targets • Accurate identify small fold changes with high accuracy of quantitation • Extensive content Over 1 8 million predesigned assays available for over 25 different species • Gold standard TaqMan qPCR chemistry TaqMan assays draw on Thermo Fisher Scientific s bioinformatics assay design pipeline to help ensure high specificity and minimal cross reactivity even for gene variants with high sequence homology • Fast delivery your assays shipped in as little as 1 2 days see below Approximate ship time • Inventoried 1 2 days in North America 3 5 days in Europe • Made to order 4 6 days in North America 6 10 days in Europe TaqMan Gene Expression assays are the gold standard in real time PCR gene expression studies built on more than 20 years of experience Each assay includes target primers and a sequence specific probe optimized for the best functional performance No additional design optimization or melt curve analysis is needed Available in a wide variety of formats and species new assay designs are constantly added to help meet your research needs TaqMan assays have been cited in over 40 000 publications and are backed by more than 350 patents All of our predesigned TaqMan Gene Expression assays are covered by the TaqMan Assays qPCR Guarantee Recommended master mix TaqMan Fast Advanced Master Mix Subject to terms and conditions For complete details go to www thermofisher com taqmanguarantee
    Catalog Number:
    4331182
    Price:
    None
    Applications:
    Industrial & Applied Science|PCR & Real-Time PCR|PCR-Based Drug Discovery Assays|Pharma & Biopharma|Real Time PCR (qPCR)|Real Time PCR-Based Gene Expression Profiling|Real-Time PCR Primers, Probes, Arrays & Controls|Two-Step qRT-PCR|Target & Lead Identification & Validation|Gene Expression Analysis & Genotyping
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    Structured Review

    Thermo Fisher fam labeled taqman probes
    TTP regulation of CXCR4 mRNA and protein. ( A ) Quantitative PCR (qPCR) quantification of CXCR4 mRNA associated with TTP protein. MDA-MB-231 cells were transfected with TTP or C124R expression plasmids for 24h. Cells were lysed, and TTP and C124R proteins were immunoprecipitated using anti-TTP or normal IgG control antibody. Quantification of associated CXCR4 mRNA was performed by qPCR using a <t>FAM-labeled</t> human CXCR4 <t>Taqman</t> expression probe and normalized to a VIC-labeled GAPDH probe. Data are from one experiment representative of two independent experiments * P
    Applied Biosystems TaqMan Gene Expression assays are used for quantitative real time PCR analysis of gene expression and consist of a pair of unlabeled PCR primers and a TaqMan probe with a dye label FAM on the 5 end and a minor groove binder MGB and non fluorescent quencher NFQ on the 3 end Features of TaqMan Gene Expression assays include • Easy to use just add cDNA and master mix and run the qPCR no melt curves required • Specific TaqMan assays use proprietary MGB containing probes that can be up to 15 bases shorter than non MGB probes improving the specificity of the assay • Sensitive TaqMan assays are ideal for measuring low levels of expression or low abundance targets • Accurate identify small fold changes with high accuracy of quantitation • Extensive content Over 1 8 million predesigned assays available for over 25 different species • Gold standard TaqMan qPCR chemistry TaqMan assays draw on Thermo Fisher Scientific s bioinformatics assay design pipeline to help ensure high specificity and minimal cross reactivity even for gene variants with high sequence homology • Fast delivery your assays shipped in as little as 1 2 days see below Approximate ship time • Inventoried 1 2 days in North America 3 5 days in Europe • Made to order 4 6 days in North America 6 10 days in Europe TaqMan Gene Expression assays are the gold standard in real time PCR gene expression studies built on more than 20 years of experience Each assay includes target primers and a sequence specific probe optimized for the best functional performance No additional design optimization or melt curve analysis is needed Available in a wide variety of formats and species new assay designs are constantly added to help meet your research needs TaqMan assays have been cited in over 40 000 publications and are backed by more than 350 patents All of our predesigned TaqMan Gene Expression assays are covered by the TaqMan Assays qPCR Guarantee Recommended master mix TaqMan Fast Advanced Master Mix Subject to terms and conditions For complete details go to www thermofisher com taqmanguarantee
    https://www.bioz.com/result/fam labeled taqman probes/product/Thermo Fisher
    Average 99 stars, based on 27 article reviews
    Price from $9.99 to $1999.99
    fam labeled taqman probes - by Bioz Stars, 2020-12
    99/100 stars

    Images

    1) Product Images from "Posttranscriptional control of the chemokine receptor CXCR4 expression in cancer cells"

    Article Title: Posttranscriptional control of the chemokine receptor CXCR4 expression in cancer cells

    Journal: Carcinogenesis

    doi: 10.1093/carcin/bgu080

    TTP regulation of CXCR4 mRNA and protein. ( A ) Quantitative PCR (qPCR) quantification of CXCR4 mRNA associated with TTP protein. MDA-MB-231 cells were transfected with TTP or C124R expression plasmids for 24h. Cells were lysed, and TTP and C124R proteins were immunoprecipitated using anti-TTP or normal IgG control antibody. Quantification of associated CXCR4 mRNA was performed by qPCR using a FAM-labeled human CXCR4 Taqman expression probe and normalized to a VIC-labeled GAPDH probe. Data are from one experiment representative of two independent experiments * P
    Figure Legend Snippet: TTP regulation of CXCR4 mRNA and protein. ( A ) Quantitative PCR (qPCR) quantification of CXCR4 mRNA associated with TTP protein. MDA-MB-231 cells were transfected with TTP or C124R expression plasmids for 24h. Cells were lysed, and TTP and C124R proteins were immunoprecipitated using anti-TTP or normal IgG control antibody. Quantification of associated CXCR4 mRNA was performed by qPCR using a FAM-labeled human CXCR4 Taqman expression probe and normalized to a VIC-labeled GAPDH probe. Data are from one experiment representative of two independent experiments * P

    Techniques Used: Real-time Polymerase Chain Reaction, Multiple Displacement Amplification, Transfection, Expressing, Immunoprecipitation, Labeling

    Related Articles

    Multiplex Assay:

    Article Title: Cystatin from Filarial Parasites Suppress the Clinical Symptoms and Pathology of Experimentally Induced Colitis in Mice by Inducing T-Regulatory Cells, B1-Cells, and Alternatively Activated Macrophages
    Article Snippet: .. Similarly, TNF-α, IL-6, and IL-10 genes were qPCR amplified from the peritoneal macrophages, using the pre-optimized TaqMan Gene expression Assays and TaqMan® multiplex master mix (Thermo Fisher Scientific, Rockford, IL, USA). ..

    Amplification:

    Article Title: Screening and identification of BP100 peptide conjugates active against Xylella fastidiosa using a viability-qPCR method
    Article Snippet: .. qPCR design: evaluation of the amplification efficiency and sensitivity qPCR assays were conducted using the primer pairs and TaqMan probe sets described in Table . .. Primer3Plus software was used to obtain amplicons with different length that shared the described forward primers and probes but with new different reverse primers.

    Article Title: Cystatin from Filarial Parasites Suppress the Clinical Symptoms and Pathology of Experimentally Induced Colitis in Mice by Inducing T-Regulatory Cells, B1-Cells, and Alternatively Activated Macrophages
    Article Snippet: .. Similarly, TNF-α, IL-6, and IL-10 genes were qPCR amplified from the peritoneal macrophages, using the pre-optimized TaqMan Gene expression Assays and TaqMan® multiplex master mix (Thermo Fisher Scientific, Rockford, IL, USA). ..

    Synthesized:

    Article Title: Interleukin‐25 initiates Th2 differentiation of human CD4+ T cells and influences expression of its own receptor
    Article Snippet: .. Complementary DNA (cDNA) was synthesized from 1 µg of RNA using the Superscript II Reverse Transcriptase according to manufacturer's instructions (Cat #18964‐014, Invitrogen, Burlington, ON, Canada). qRT‐PCR TaqMan gene expression assays for CRTh2 (Hs00173717_m1), IL‐25R (Hs00218889_1) and IL‐4 (Hs00174122_m1) were purchased from Applied Biosystems (Burlington, On, Canada). .. The PCR program was 2 min at 50°C, 10 min at 95°C, 40 cycles of 15 sec at 95°C, 1 min at 60°C (Eppendorf RealPlex 4, Mississauga, ON).

    Quantitative RT-PCR:

    Article Title: Interleukin‐25 initiates Th2 differentiation of human CD4+ T cells and influences expression of its own receptor
    Article Snippet: .. Complementary DNA (cDNA) was synthesized from 1 µg of RNA using the Superscript II Reverse Transcriptase according to manufacturer's instructions (Cat #18964‐014, Invitrogen, Burlington, ON, Canada). qRT‐PCR TaqMan gene expression assays for CRTh2 (Hs00173717_m1), IL‐25R (Hs00218889_1) and IL‐4 (Hs00174122_m1) were purchased from Applied Biosystems (Burlington, On, Canada). .. The PCR program was 2 min at 50°C, 10 min at 95°C, 40 cycles of 15 sec at 95°C, 1 min at 60°C (Eppendorf RealPlex 4, Mississauga, ON).

    Article Title: The polycomb group protein BMI-1 inhibitor PTC-209 is a potent anti-myeloma agent alone or in combination with epigenetic inhibitors targeting EZH2 and the BET bromodomains
    Article Snippet: .. RT-qPCR analysis of mRNA was performed using TaqMan® gene expression assays (Applied Biosystems) for BMI-1 (Assay ID: Hs00995536_m1, Catalog #: 4448892), BIM (Assay ID: Hs00708019_s1, Catalog #: 4453320) and Actin (Assay ID: Hs01060665_g1, Catalog #: 4448892)as housekeeping mRNA. ..

    Article Title: Upregulation of cyclin-dependent kinase inhibitors CDKN1B and CDKN1C in hepatocellular carcinoma-derived cells via goniothalamin-mediated protein stabilization and epigenetic modifications
    Article Snippet: .. TaqMan® chemistry with primers and probes (Life Technologies): CDKN1B (#4331182; 151 bp, Hs01597588_m1, NM_004064.3 ), CDKN1C (#4331182; 91 bp, Hs00175938_m1, NM_000076.2 , NM_001122630.1 , NM_001122631.1 ), SKP2 (#4331182; 59 bp, Hs01021864_m1, NM_001243120.1 , NM_005983.3 , NM_032637.3 ) and GAPDH (#4453320; 93 bp, Hs02758991_g1, NM_001256799.1 , NM_002046.4 ) were used for quantitative RT-PCR. .. The relative expression folds of each target transcript were given by 2−ΔΔCT , where ΔΔC T = ΔC T (treatment) – ΔC T (DMSO); ΔC T represented the C T of a target transcript subtracted from the C T of GAPDH (internal control).

    Real-time Polymerase Chain Reaction:

    Article Title: Screening and identification of BP100 peptide conjugates active against Xylella fastidiosa using a viability-qPCR method
    Article Snippet: .. qPCR design: evaluation of the amplification efficiency and sensitivity qPCR assays were conducted using the primer pairs and TaqMan probe sets described in Table . .. Primer3Plus software was used to obtain amplicons with different length that shared the described forward primers and probes but with new different reverse primers.

    Article Title: High glucose concentrations induce TNF-? production through the down-regulation of CD33 in primary human monocytes
    Article Snippet: .. Real-time PCR reactions were performed in duplicate wells, according to the protocols for Taqman gene assays for CD33 (Hs00233544_m1), TNF-α (Hs01000485_m1), IL-1β (IHs0174097_m1), IL-6 (Hs00985639_m1), SOCS-3 (Hs01000485_g1), and 18 S ribosomal RNA (Applied Biosystems, Carlsbad, CA). ..

    Article Title: Cystatin from Filarial Parasites Suppress the Clinical Symptoms and Pathology of Experimentally Induced Colitis in Mice by Inducing T-Regulatory Cells, B1-Cells, and Alternatively Activated Macrophages
    Article Snippet: .. Similarly, TNF-α, IL-6, and IL-10 genes were qPCR amplified from the peritoneal macrophages, using the pre-optimized TaqMan Gene expression Assays and TaqMan® multiplex master mix (Thermo Fisher Scientific, Rockford, IL, USA). ..

    Expressing:

    Article Title: Interleukin‐25 initiates Th2 differentiation of human CD4+ T cells and influences expression of its own receptor
    Article Snippet: .. Complementary DNA (cDNA) was synthesized from 1 µg of RNA using the Superscript II Reverse Transcriptase according to manufacturer's instructions (Cat #18964‐014, Invitrogen, Burlington, ON, Canada). qRT‐PCR TaqMan gene expression assays for CRTh2 (Hs00173717_m1), IL‐25R (Hs00218889_1) and IL‐4 (Hs00174122_m1) were purchased from Applied Biosystems (Burlington, On, Canada). .. The PCR program was 2 min at 50°C, 10 min at 95°C, 40 cycles of 15 sec at 95°C, 1 min at 60°C (Eppendorf RealPlex 4, Mississauga, ON).

    Article Title: Determination of the physiological and pathological roles of E2F3 in adult tissues
    Article Snippet: .. For Taqman gene expression assays, the following commercial primer/probe sets were used: Actin (4352933E, Applied Biosystems), Mboat1 (4331182, Applied Biosystems) and Cdkal1 (4351372, Applied Biosystems). ..

    Article Title: Cystatin from Filarial Parasites Suppress the Clinical Symptoms and Pathology of Experimentally Induced Colitis in Mice by Inducing T-Regulatory Cells, B1-Cells, and Alternatively Activated Macrophages
    Article Snippet: .. Similarly, TNF-α, IL-6, and IL-10 genes were qPCR amplified from the peritoneal macrophages, using the pre-optimized TaqMan Gene expression Assays and TaqMan® multiplex master mix (Thermo Fisher Scientific, Rockford, IL, USA). ..

    Article Title: The polycomb group protein BMI-1 inhibitor PTC-209 is a potent anti-myeloma agent alone or in combination with epigenetic inhibitors targeting EZH2 and the BET bromodomains
    Article Snippet: .. RT-qPCR analysis of mRNA was performed using TaqMan® gene expression assays (Applied Biosystems) for BMI-1 (Assay ID: Hs00995536_m1, Catalog #: 4448892), BIM (Assay ID: Hs00708019_s1, Catalog #: 4453320) and Actin (Assay ID: Hs01060665_g1, Catalog #: 4448892)as housekeeping mRNA. ..

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  • 96
    Thermo Fisher gene exp camp hs00189038 m1
    Comparison of iSS-predicted effects of 25OHD or 1,25(OH) 2 D on monocyte expression of <t>CAMP</t> with observed in vitro responses of monocytes to treatment with these metabolites. Adherent human monocytes were incubated for 6 hrs in media containing 5% serum with doses of (A) 25OHD (1–300 nM) and (B) 1,25(OH) 2 D (0.1–6 nM). The experimental data is indicated by blue dots and error bars (± SD). Black lines indicate data predicted by the iSS mathematical model assuming basal levels of VDR and CYP27B1 (i.e. no activation). For the purpose of this modeling, DBP was represented by the GC1F/1F allelic combination.
    Gene Exp Camp Hs00189038 M1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 26 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gene exp camp hs00189038 m1/product/Thermo Fisher
    Average 96 stars, based on 26 article reviews
    Price from $9.99 to $1999.99
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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
    Price from $9.99 to $1999.99
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    86
    Thermo Fisher gene exp trp53 mm00441964 g1
    MPNSTs occurring in P 0 -GGFβ3; <t>Trp53</t> +/− mice develop within peripheral nervous system ganglia. a : A markedly hypercellular microtumor developing within the trigeminal ganglion of a P 0 -GGFβ3; Trp53 +/− mouse. Scale bar, 100µm.
    Gene Exp Trp53 Mm00441964 G1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/gene exp trp53 mm00441964 g1/product/Thermo Fisher
    Average 86 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
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    Image Search Results


    Comparison of iSS-predicted effects of 25OHD or 1,25(OH) 2 D on monocyte expression of CAMP with observed in vitro responses of monocytes to treatment with these metabolites. Adherent human monocytes were incubated for 6 hrs in media containing 5% serum with doses of (A) 25OHD (1–300 nM) and (B) 1,25(OH) 2 D (0.1–6 nM). The experimental data is indicated by blue dots and error bars (± SD). Black lines indicate data predicted by the iSS mathematical model assuming basal levels of VDR and CYP27B1 (i.e. no activation). For the purpose of this modeling, DBP was represented by the GC1F/1F allelic combination.

    Journal: PLoS ONE

    Article Title: Vitamin D Binding Protein and Monocyte Response to 25-Hydroxyvitamin D and 1,25-Dihydroxyvitamin D: Analysis by Mathematical Modeling

    doi: 10.1371/journal.pone.0030773

    Figure Lengend Snippet: Comparison of iSS-predicted effects of 25OHD or 1,25(OH) 2 D on monocyte expression of CAMP with observed in vitro responses of monocytes to treatment with these metabolites. Adherent human monocytes were incubated for 6 hrs in media containing 5% serum with doses of (A) 25OHD (1–300 nM) and (B) 1,25(OH) 2 D (0.1–6 nM). The experimental data is indicated by blue dots and error bars (± SD). Black lines indicate data predicted by the iSS mathematical model assuming basal levels of VDR and CYP27B1 (i.e. no activation). For the purpose of this modeling, DBP was represented by the GC1F/1F allelic combination.

    Article Snippet: Specifically, we utilized FAM-labeled TaqMan Gene Expression Assay probe/primer Hs00189038_m1 (CAMP) in conjunction with VIC/MGB Probe/Primer Eukaryotic 18S rRNA Endogenous Control (part number 4319413E) as the internal calibrator.

    Techniques: Expressing, In Vitro, Incubation, Activation Assay

    Schematic framework of parameters used to produce extracellular steady state (eSS) and intracellular (iSS) mathematical models for vitamin D metabolism and function. Free 25OHD and 1,25(OH) 2 D interacting with extra-cellular vitamin D binding protein (DBP) or albumin indicated in black text and arrows (eSS model). Intra-cellular interactions involving the vitamin D-activating enzyme (CYP27B1), the vitamin D receptor (VDR) and transcriptional induction of the antibacterial protein CAMP via interaction between VDR and the CAMP gene promoter (CAMP-DNA) indicated by grey text and arrows (iSS model).

    Journal: PLoS ONE

    Article Title: Vitamin D Binding Protein and Monocyte Response to 25-Hydroxyvitamin D and 1,25-Dihydroxyvitamin D: Analysis by Mathematical Modeling

    doi: 10.1371/journal.pone.0030773

    Figure Lengend Snippet: Schematic framework of parameters used to produce extracellular steady state (eSS) and intracellular (iSS) mathematical models for vitamin D metabolism and function. Free 25OHD and 1,25(OH) 2 D interacting with extra-cellular vitamin D binding protein (DBP) or albumin indicated in black text and arrows (eSS model). Intra-cellular interactions involving the vitamin D-activating enzyme (CYP27B1), the vitamin D receptor (VDR) and transcriptional induction of the antibacterial protein CAMP via interaction between VDR and the CAMP gene promoter (CAMP-DNA) indicated by grey text and arrows (iSS model).

    Article Snippet: Specifically, we utilized FAM-labeled TaqMan Gene Expression Assay probe/primer Hs00189038_m1 (CAMP) in conjunction with VIC/MGB Probe/Primer Eukaryotic 18S rRNA Endogenous Control (part number 4319413E) as the internal calibrator.

    Techniques: Binding Assay

    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

    MPNSTs occurring in P 0 -GGFβ3; Trp53 +/− mice develop within peripheral nervous system ganglia. a : A markedly hypercellular microtumor developing within the trigeminal ganglion of a P 0 -GGFβ3; Trp53 +/− mouse. Scale bar, 100µm.

    Journal: Acta neuropathologica

    Article Title: Neuregulin-1 overexpression and Trp53 haploinsufficiency cooperatively promote de novo malignant peripheral nerve sheath tumor pathogenesis

    doi: 10.1007/s00401-013-1209-3

    Figure Lengend Snippet: MPNSTs occurring in P 0 -GGFβ3; Trp53 +/− mice develop within peripheral nervous system ganglia. a : A markedly hypercellular microtumor developing within the trigeminal ganglion of a P 0 -GGFβ3; Trp53 +/− mouse. Scale bar, 100µm.

    Article Snippet: Assays of Trp53 transcripts were performed using FAM-labeled TaqMan MGB probes (ABI assay Mm00441964_g1).

    Techniques: Mouse Assay

    Ki67 labeling indices in the microtumors occurring in P 0 -GGFβ3; Trp53 +/− mice are higher than seen in neurofibromas and non-neoplastic ganglia but lower than is seen in the larger tumors present in these animals. a, b : Major MPNST ( a )

    Journal: Acta neuropathologica

    Article Title: Neuregulin-1 overexpression and Trp53 haploinsufficiency cooperatively promote de novo malignant peripheral nerve sheath tumor pathogenesis

    doi: 10.1007/s00401-013-1209-3

    Figure Lengend Snippet: Ki67 labeling indices in the microtumors occurring in P 0 -GGFβ3; Trp53 +/− mice are higher than seen in neurofibromas and non-neoplastic ganglia but lower than is seen in the larger tumors present in these animals. a, b : Major MPNST ( a )

    Article Snippet: Assays of Trp53 transcripts were performed using FAM-labeled TaqMan MGB probes (ABI assay Mm00441964_g1).

    Techniques: Labeling, Mouse Assay

    Whole Genome Array Comparative Genomic Hybridization Indicates that Copy Number Variations in Low Grade P0 -GGFβ3; Trp53 +/− MPNSTs Are Less Extensive Than Those in P0 -GGFβ3 MPNSTs

    Journal: Acta neuropathologica

    Article Title: Neuregulin-1 overexpression and Trp53 haploinsufficiency cooperatively promote de novo malignant peripheral nerve sheath tumor pathogenesis

    doi: 10.1007/s00401-013-1209-3

    Figure Lengend Snippet: Whole Genome Array Comparative Genomic Hybridization Indicates that Copy Number Variations in Low Grade P0 -GGFβ3; Trp53 +/− MPNSTs Are Less Extensive Than Those in P0 -GGFβ3 MPNSTs

    Article Snippet: Assays of Trp53 transcripts were performed using FAM-labeled TaqMan MGB probes (ABI assay Mm00441964_g1).

    Techniques: Hybridization

    Haploinsufficiency for Trp53 , but not Nf1 , impairs survival in the presence of NRG 1 overexpression. a : Kaplan-Meier curve indicating the survival rates of P 0 -GGFβ3, Nf1 +/− and P 0 -GGFβ3; Nf1 +/− mice over the first year of

    Journal: Acta neuropathologica

    Article Title: Neuregulin-1 overexpression and Trp53 haploinsufficiency cooperatively promote de novo malignant peripheral nerve sheath tumor pathogenesis

    doi: 10.1007/s00401-013-1209-3

    Figure Lengend Snippet: Haploinsufficiency for Trp53 , but not Nf1 , impairs survival in the presence of NRG 1 overexpression. a : Kaplan-Meier curve indicating the survival rates of P 0 -GGFβ3, Nf1 +/− and P 0 -GGFβ3; Nf1 +/− mice over the first year of

    Article Snippet: Assays of Trp53 transcripts were performed using FAM-labeled TaqMan MGB probes (ABI assay Mm00441964_g1).

    Techniques: Over Expression, Mouse Assay

    P 0 -GGFβ3; Trp53 +/− mice develop MPNSTs, but not neurofibromas. a : In situ gross image of two independently arising trigeminal tumors. b–d : Hematoxylin and eosin stained sections of MPNSTs arising in P 0 -GGFβ3; Trp53 +/−

    Journal: Acta neuropathologica

    Article Title: Neuregulin-1 overexpression and Trp53 haploinsufficiency cooperatively promote de novo malignant peripheral nerve sheath tumor pathogenesis

    doi: 10.1007/s00401-013-1209-3

    Figure Lengend Snippet: P 0 -GGFβ3; Trp53 +/− mice develop MPNSTs, but not neurofibromas. a : In situ gross image of two independently arising trigeminal tumors. b–d : Hematoxylin and eosin stained sections of MPNSTs arising in P 0 -GGFβ3; Trp53 +/−

    Article Snippet: Assays of Trp53 transcripts were performed using FAM-labeled TaqMan MGB probes (ABI assay Mm00441964_g1).

    Techniques: Mouse Assay, In Situ, Staining

    Early passage P 0 -GGFβ3; Trp53 +/− MPNST cultures consistently express Schwann cell markers and variably express neuronal and muscle markers. a : RT-PCR of Schwann cell (blue), neuronal (red), and muscle (green) markers expressed in passage

    Journal: Acta neuropathologica

    Article Title: Neuregulin-1 overexpression and Trp53 haploinsufficiency cooperatively promote de novo malignant peripheral nerve sheath tumor pathogenesis

    doi: 10.1007/s00401-013-1209-3

    Figure Lengend Snippet: Early passage P 0 -GGFβ3; Trp53 +/− MPNST cultures consistently express Schwann cell markers and variably express neuronal and muscle markers. a : RT-PCR of Schwann cell (blue), neuronal (red), and muscle (green) markers expressed in passage

    Article Snippet: Assays of Trp53 transcripts were performed using FAM-labeled TaqMan MGB probes (ABI assay Mm00441964_g1).

    Techniques: Reverse Transcription Polymerase Chain Reaction

    ErbB-dependent Ras hyperactivation and persistent Trp53 haploinsufficiency is evident in P 0 -GGFβ3; Trp53 +/− MPNSTs. a : Ras activity is increased in the MPNSTs compared to Schwann cells and this activity is attenuated by treatment with the

    Journal: Acta neuropathologica

    Article Title: Neuregulin-1 overexpression and Trp53 haploinsufficiency cooperatively promote de novo malignant peripheral nerve sheath tumor pathogenesis

    doi: 10.1007/s00401-013-1209-3

    Figure Lengend Snippet: ErbB-dependent Ras hyperactivation and persistent Trp53 haploinsufficiency is evident in P 0 -GGFβ3; Trp53 +/− MPNSTs. a : Ras activity is increased in the MPNSTs compared to Schwann cells and this activity is attenuated by treatment with the

    Article Snippet: Assays of Trp53 transcripts were performed using FAM-labeled TaqMan MGB probes (ABI assay Mm00441964_g1).

    Techniques: Activity Assay

    Overexpression of Type II NRG1 Interacts with Trp53 , but not Nf1 , Haploinsufficiency, to Promote MPNST Pathogenesis

    Journal: Acta neuropathologica

    Article Title: Neuregulin-1 overexpression and Trp53 haploinsufficiency cooperatively promote de novo malignant peripheral nerve sheath tumor pathogenesis

    doi: 10.1007/s00401-013-1209-3

    Figure Lengend Snippet: Overexpression of Type II NRG1 Interacts with Trp53 , but not Nf1 , Haploinsufficiency, to Promote MPNST Pathogenesis

    Article Snippet: Assays of Trp53 transcripts were performed using FAM-labeled TaqMan MGB probes (ABI assay Mm00441964_g1).

    Techniques: Over Expression