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luciferase validation vector ori empty plasmid  (Addgene inc)


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    Addgene inc luciferase validation vector ori empty plasmid
    Luciferase Validation Vector Ori Empty Plasmid, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/starr+seq+vector/STARR-seq+luciferase+validation+vector_mP_empty+(Plasmid+%2399298)/pmc09712620-220-10-16
    Average 93 stars, based on 2 article reviews
    luciferase validation vector ori empty plasmid - by Bioz Stars, 2026-10
    93/100 stars

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    Related Articles

    Amplification:

    Article Title: Estrogen Receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
    Article Snippet: For luciferase assays the regions of interest (WT) were PCR amplified from pooled male human genomic DNA (Promega). .. The amplified regions were cloned by Gibson assembly into a STARR luciferase vector ORI empty plasmid (Addgene #99298) (Muerdter et al. 2018) using the NEBuilder HiFi DNA Assembly master mix (NEB). ..

    Article Title: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions.
    Article Snippet: breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions Stacey E.P.. Joosten, Sebastian Gregoricchio, Suzan Stelloo, Elif Yapıcı, Chia-Chi Flora Huang, Kerim Yavuz, Maria Donaldson Collier, Tunç Morova, Umut Berkay Altintas,̧ Yongsoo Kim, Sander Canisius, Cathy B. Moelans, Paul J. van Diest, Gozde Korkmaz, Nathan A.. Lack, Michiel Vermeulen, Sabine C. Linn, and Wilbert Zwart Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Oncode Institute, The Netherlands; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands; Koç University School of Medicine, 34450 Istanbul, Turkey; Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey; Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada; Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands; Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Medical Oncology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands

    Article Title: Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential
    Article Snippet: For performing luciferase assays, regions of interest were PCR amplified from pooled male human genomic DNA (Promega) with overhangs added for Gibson assembly. .. The amplified regions were then cloned into a modified STARR luciferase validation vector ORI empty plasmid (Addgene #99298) using the NEBuilder HiFi DNA Assembly master mix (NEB). ..

    Clone Assay:

    Article Title: Estrogen Receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
    Article Snippet: For luciferase assays the regions of interest (WT) were PCR amplified from pooled male human genomic DNA (Promega). .. The amplified regions were cloned by Gibson assembly into a STARR luciferase vector ORI empty plasmid (Addgene #99298) (Muerdter et al. 2018) using the NEBuilder HiFi DNA Assembly master mix (NEB). ..

    Article Title: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions.
    Article Snippet: breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions Stacey E.P.. Joosten, Sebastian Gregoricchio, Suzan Stelloo, Elif Yapıcı, Chia-Chi Flora Huang, Kerim Yavuz, Maria Donaldson Collier, Tunç Morova, Umut Berkay Altintas,̧ Yongsoo Kim, Sander Canisius, Cathy B. Moelans, Paul J. van Diest, Gozde Korkmaz, Nathan A.. Lack, Michiel Vermeulen, Sabine C. Linn, and Wilbert Zwart Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Oncode Institute, The Netherlands; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands; Koç University School of Medicine, 34450 Istanbul, Turkey; Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey; Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada; Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands; Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Medical Oncology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands

    Article Title: Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential
    Article Snippet: For performing luciferase assays, regions of interest were PCR amplified from pooled male human genomic DNA (Promega) with overhangs added for Gibson assembly. .. The amplified regions were then cloned into a modified STARR luciferase validation vector ORI empty plasmid (Addgene #99298) using the NEBuilder HiFi DNA Assembly master mix (NEB). ..

    Luciferase:

    Article Title: Estrogen Receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
    Article Snippet: For luciferase assays the regions of interest (WT) were PCR amplified from pooled male human genomic DNA (Promega). .. The amplified regions were cloned by Gibson assembly into a STARR luciferase vector ORI empty plasmid (Addgene #99298) (Muerdter et al. 2018) using the NEBuilder HiFi DNA Assembly master mix (NEB). ..

    Article Title: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions.
    Article Snippet: breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions Stacey E.P.. Joosten, Sebastian Gregoricchio, Suzan Stelloo, Elif Yapıcı, Chia-Chi Flora Huang, Kerim Yavuz, Maria Donaldson Collier, Tunç Morova, Umut Berkay Altintas,̧ Yongsoo Kim, Sander Canisius, Cathy B. Moelans, Paul J. van Diest, Gozde Korkmaz, Nathan A.. Lack, Michiel Vermeulen, Sabine C. Linn, and Wilbert Zwart Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Oncode Institute, The Netherlands; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands; Koç University School of Medicine, 34450 Istanbul, Turkey; Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey; Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada; Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands; Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Medical Oncology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands

    Article Title: Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential
    Article Snippet: For performing luciferase assays, regions of interest were PCR amplified from pooled male human genomic DNA (Promega) with overhangs added for Gibson assembly. .. The amplified regions were then cloned into a modified STARR luciferase validation vector ORI empty plasmid (Addgene #99298) using the NEBuilder HiFi DNA Assembly master mix (NEB). ..

    Plasmid Preparation:

    Article Title: Estrogen Receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
    Article Snippet: For luciferase assays the regions of interest (WT) were PCR amplified from pooled male human genomic DNA (Promega). .. The amplified regions were cloned by Gibson assembly into a STARR luciferase vector ORI empty plasmid (Addgene #99298) (Muerdter et al. 2018) using the NEBuilder HiFi DNA Assembly master mix (NEB). ..

    Article Title: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions.
    Article Snippet: breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions Stacey E.P.. Joosten, Sebastian Gregoricchio, Suzan Stelloo, Elif Yapıcı, Chia-Chi Flora Huang, Kerim Yavuz, Maria Donaldson Collier, Tunç Morova, Umut Berkay Altintas,̧ Yongsoo Kim, Sander Canisius, Cathy B. Moelans, Paul J. van Diest, Gozde Korkmaz, Nathan A.. Lack, Michiel Vermeulen, Sabine C. Linn, and Wilbert Zwart Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Oncode Institute, The Netherlands; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands; Koç University School of Medicine, 34450 Istanbul, Turkey; Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey; Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada; Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands; Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Medical Oncology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands

    Article Title: Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential
    Article Snippet: For performing luciferase assays, regions of interest were PCR amplified from pooled male human genomic DNA (Promega) with overhangs added for Gibson assembly. .. The amplified regions were then cloned into a modified STARR luciferase validation vector ORI empty plasmid (Addgene #99298) using the NEBuilder HiFi DNA Assembly master mix (NEB). ..

    Modification:

    Article Title: Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential
    Article Snippet: For performing luciferase assays, regions of interest were PCR amplified from pooled male human genomic DNA (Promega) with overhangs added for Gibson assembly. .. The amplified regions were then cloned into a modified STARR luciferase validation vector ORI empty plasmid (Addgene #99298) using the NEBuilder HiFi DNA Assembly master mix (NEB). ..

    Biomarker Discovery:

    Article Title: Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential
    Article Snippet: For performing luciferase assays, regions of interest were PCR amplified from pooled male human genomic DNA (Promega) with overhangs added for Gibson assembly. .. The amplified regions were then cloned into a modified STARR luciferase validation vector ORI empty plasmid (Addgene #99298) using the NEBuilder HiFi DNA Assembly master mix (NEB). ..



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    Novel motifs affect gene transcription in Jurkats. A Shown, is a diagram of <t>the</t> <t>STARR-seq</t> oligo library design. The figure was adapted from Georgakopoulos-Soares et al under the Creative Commons license http://creativecommons.org/licenses/by/4.0/ . Changes were made to the figure to account for the differences in our overall library design. Eighteen candidate motifs (nine novel and nine TFBS motifs) were embedded in a synthetic background DNA sequence. Each sequence contained one to three instances of a motif, separated by 10bp. The oligonucleotide library contains every possible combination, position, and orientation of the 18 candidate motifs. B The mean activity score for the 18 motifs in their respective orientations for Jurkat and ( C ) K562 cells are shown above. Mean activity scores were obtained from oligos containing the motif of interest only in its indicated orientation. Motifs with a significant effect on gene transcription were identified using a two-sided t-test that compared oligos containing the motif of interest to those that do not contain the motif. Only oligos containing 1-3 instances of the given motif in its respective orientation were used. Motifs with a significant effect of gene transcription are indicated as solid bars (Bonferroni corrected, p -value < 0.001, |Cohen's D| > 0.5). Error bars represent the standard error of activity scores. D Linear modelling was used to determine if there was an association between the number of copies of a motif and the mean activity score for the motifs with a significant effect on gene transcription in Jurkat cells and ( E ) K562 cells (Bonferroni corrected, p -value < 0.007). Only oligos containing one to three copies of the motif of interest were included in the analysis
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    Image Search Results


    Novel motifs affect gene transcription in Jurkats. A Shown, is a diagram of the STARR-seq oligo library design. The figure was adapted from Georgakopoulos-Soares et al under the Creative Commons license http://creativecommons.org/licenses/by/4.0/ . Changes were made to the figure to account for the differences in our overall library design. Eighteen candidate motifs (nine novel and nine TFBS motifs) were embedded in a synthetic background DNA sequence. Each sequence contained one to three instances of a motif, separated by 10bp. The oligonucleotide library contains every possible combination, position, and orientation of the 18 candidate motifs. B The mean activity score for the 18 motifs in their respective orientations for Jurkat and ( C ) K562 cells are shown above. Mean activity scores were obtained from oligos containing the motif of interest only in its indicated orientation. Motifs with a significant effect on gene transcription were identified using a two-sided t-test that compared oligos containing the motif of interest to those that do not contain the motif. Only oligos containing 1-3 instances of the given motif in its respective orientation were used. Motifs with a significant effect of gene transcription are indicated as solid bars (Bonferroni corrected, p -value < 0.001, |Cohen's D| > 0.5). Error bars represent the standard error of activity scores. D Linear modelling was used to determine if there was an association between the number of copies of a motif and the mean activity score for the motifs with a significant effect on gene transcription in Jurkat cells and ( E ) K562 cells (Bonferroni corrected, p -value < 0.007). Only oligos containing one to three copies of the motif of interest were included in the analysis

    Journal: BMC Genomics

    Article Title: Identification of novel DNA sequence motifs that modulate transcription in T cells

    doi: 10.1186/s12864-025-12425-9

    Figure Lengend Snippet: Novel motifs affect gene transcription in Jurkats. A Shown, is a diagram of the STARR-seq oligo library design. The figure was adapted from Georgakopoulos-Soares et al under the Creative Commons license http://creativecommons.org/licenses/by/4.0/ . Changes were made to the figure to account for the differences in our overall library design. Eighteen candidate motifs (nine novel and nine TFBS motifs) were embedded in a synthetic background DNA sequence. Each sequence contained one to three instances of a motif, separated by 10bp. The oligonucleotide library contains every possible combination, position, and orientation of the 18 candidate motifs. B The mean activity score for the 18 motifs in their respective orientations for Jurkat and ( C ) K562 cells are shown above. Mean activity scores were obtained from oligos containing the motif of interest only in its indicated orientation. Motifs with a significant effect on gene transcription were identified using a two-sided t-test that compared oligos containing the motif of interest to those that do not contain the motif. Only oligos containing 1-3 instances of the given motif in its respective orientation were used. Motifs with a significant effect of gene transcription are indicated as solid bars (Bonferroni corrected, p -value < 0.001, |Cohen's D| > 0.5). Error bars represent the standard error of activity scores. D Linear modelling was used to determine if there was an association between the number of copies of a motif and the mean activity score for the motifs with a significant effect on gene transcription in Jurkat cells and ( E ) K562 cells (Bonferroni corrected, p -value < 0.007). Only oligos containing one to three copies of the motif of interest were included in the analysis

    Article Snippet: After designing the library, the oligonucleotide sequences were flanked by AgeI and SalI restriction sites to facilitate cloning into the STARR-seq vector (hSTARR-seq_ORI, Addgene #99296) and the necessary priming and Illumina adapter sequences were added to enable sequencing (Supplemental Table S3).

    Techniques: Sequencing, Activity Assay