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starr seq luciferase validation vector  (Addgene inc)


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    Addgene inc starr seq luciferase validation vector
    Starr Seq Luciferase Validation Vector, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/starr+seq+vector/STARR-seq+luciferase+validation+vector_ORI_neg%2Econt+(Plasmid+%2399315)/pm36113676-99-30-34
    Average 93 stars, based on 4 article reviews
    starr seq luciferase validation vector - by Bioz Stars, 2026-09
    93/100 stars

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    Related Articles

    Construct:

    Article Title: Long-range interaction within the chromatin domain determines regulatory patterns in porcine skeletal muscle.
    Article Snippet: .. LUC-ENH and LUC-CON plasmids were constructed by cloning the purified enhancer and control sequence amplified from pig genomic DNA to the MfeI (NEB) and SalI (NEB) restriction enzyme sites of STARR-seq luciferase validation vector (Addgene). .. LUC-ENH, LUC-CON and plasmid without inserted fragments (named LUCMOCK) were co-transfected with pRL-TK plasmid (BNCC) into mouse C2C12 cells (ATCC) and pig IPEC-J2 cells (BNCC) and PK-15 cells (ATCC), respectively.

    Cloning:

    Article Title: Long-range interaction within the chromatin domain determines regulatory patterns in porcine skeletal muscle.
    Article Snippet: .. LUC-ENH and LUC-CON plasmids were constructed by cloning the purified enhancer and control sequence amplified from pig genomic DNA to the MfeI (NEB) and SalI (NEB) restriction enzyme sites of STARR-seq luciferase validation vector (Addgene). .. LUC-ENH, LUC-CON and plasmid without inserted fragments (named LUCMOCK) were co-transfected with pRL-TK plasmid (BNCC) into mouse C2C12 cells (ATCC) and pig IPEC-J2 cells (BNCC) and PK-15 cells (ATCC), respectively.

    Purification:

    Article Title: Long-range interaction within the chromatin domain determines regulatory patterns in porcine skeletal muscle.
    Article Snippet: .. LUC-ENH and LUC-CON plasmids were constructed by cloning the purified enhancer and control sequence amplified from pig genomic DNA to the MfeI (NEB) and SalI (NEB) restriction enzyme sites of STARR-seq luciferase validation vector (Addgene). .. LUC-ENH, LUC-CON and plasmid without inserted fragments (named LUCMOCK) were co-transfected with pRL-TK plasmid (BNCC) into mouse C2C12 cells (ATCC) and pig IPEC-J2 cells (BNCC) and PK-15 cells (ATCC), respectively.

    Control:

    Article Title: Long-range interaction within the chromatin domain determines regulatory patterns in porcine skeletal muscle.
    Article Snippet: .. LUC-ENH and LUC-CON plasmids were constructed by cloning the purified enhancer and control sequence amplified from pig genomic DNA to the MfeI (NEB) and SalI (NEB) restriction enzyme sites of STARR-seq luciferase validation vector (Addgene). .. LUC-ENH, LUC-CON and plasmid without inserted fragments (named LUCMOCK) were co-transfected with pRL-TK plasmid (BNCC) into mouse C2C12 cells (ATCC) and pig IPEC-J2 cells (BNCC) and PK-15 cells (ATCC), respectively.

    Article Title: Identification of ALK in Thinness.
    Article Snippet: .. Enhancer (luciferase reporter) assay 5x105 SH-SY5Y cells (Sigma #94030304) were electroporated via Maxcyte STX (Cat No. GOC1) with the ‘‘luciferase reporter vector’’ (Addgene ID #99297) utilizing the ORI as a core promoter (Muerdter et al., 2018) comprising either the putative identified enhancer region spanning the ALK indel rs568057364 or a negative control (Addgene ID #99315) together with a Renilla control vector (Promega # E2261) in a ratio of 10 to 1. ..

    Sequencing:

    Article Title: Long-range interaction within the chromatin domain determines regulatory patterns in porcine skeletal muscle.
    Article Snippet: .. LUC-ENH and LUC-CON plasmids were constructed by cloning the purified enhancer and control sequence amplified from pig genomic DNA to the MfeI (NEB) and SalI (NEB) restriction enzyme sites of STARR-seq luciferase validation vector (Addgene). .. LUC-ENH, LUC-CON and plasmid without inserted fragments (named LUCMOCK) were co-transfected with pRL-TK plasmid (BNCC) into mouse C2C12 cells (ATCC) and pig IPEC-J2 cells (BNCC) and PK-15 cells (ATCC), respectively.

    Article Title: Widespread Long-range Cis-Regulatory Elements in the Maize Genome
    Article Snippet: .. The STARR-seq plasmid sequence and additional information can be found at Addgene, deposit number 117379 ( https://www.addgene.org/117379/ ), where it is available for purchase. .. Competing Interests Robert J Schmitz and Xiaoyu Zhang are co-founders of REquest Genomics, LLC, a company that provides epigenomics services.

    Article Title: Widespread Long-range Cis-Regulatory Elements in the Maize Genome
    Article Snippet: .. Our STARR-seq plasmid sequence and additional information can be found at Addgene, deposit number 117379 ( https://www.addgene.org/117379/ ). .. The genomic DNA input for the STARR-seq assay was a ~150 kb bacterial artifical chromosome CH201-136H12 ( https://www.maizegdb.org/data_center/bac?id=613738 ) and an ATAC-seq library derived from maize second leaves.

    Amplification:

    Article Title: Long-range interaction within the chromatin domain determines regulatory patterns in porcine skeletal muscle.
    Article Snippet: .. LUC-ENH and LUC-CON plasmids were constructed by cloning the purified enhancer and control sequence amplified from pig genomic DNA to the MfeI (NEB) and SalI (NEB) restriction enzyme sites of STARR-seq luciferase validation vector (Addgene). .. LUC-ENH, LUC-CON and plasmid without inserted fragments (named LUCMOCK) were co-transfected with pRL-TK plasmid (BNCC) into mouse C2C12 cells (ATCC) and pig IPEC-J2 cells (BNCC) and PK-15 cells (ATCC), respectively.

    Luciferase:

    Article Title: Long-range interaction within the chromatin domain determines regulatory patterns in porcine skeletal muscle.
    Article Snippet: .. LUC-ENH and LUC-CON plasmids were constructed by cloning the purified enhancer and control sequence amplified from pig genomic DNA to the MfeI (NEB) and SalI (NEB) restriction enzyme sites of STARR-seq luciferase validation vector (Addgene). .. LUC-ENH, LUC-CON and plasmid without inserted fragments (named LUCMOCK) were co-transfected with pRL-TK plasmid (BNCC) into mouse C2C12 cells (ATCC) and pig IPEC-J2 cells (BNCC) and PK-15 cells (ATCC), respectively.

    Article Title: Identification of ALK in Thinness.
    Article Snippet: .. Enhancer (luciferase reporter) assay 5x105 SH-SY5Y cells (Sigma #94030304) were electroporated via Maxcyte STX (Cat No. GOC1) with the ‘‘luciferase reporter vector’’ (Addgene ID #99297) utilizing the ORI as a core promoter (Muerdter et al., 2018) comprising either the putative identified enhancer region spanning the ALK indel rs568057364 or a negative control (Addgene ID #99315) together with a Renilla control vector (Promega # E2261) in a ratio of 10 to 1. ..

    Article Title: Glucocorticoids unmask silent non-coding genetic risk variants for common diseases
    Article Snippet: .. To validate selected STARR-seq signals with clinical significance, we conducted luciferase reporter gene assays using the STARR-seq luciferase validation vector (Addgene #9927). .. The plasmid was digested with restriction enzymes BamHI-HF® (Cat#: R3136S, NEB) and SspI-HF® (Cat#: R3132S, NEB).

    Biomarker Discovery:

    Article Title: Long-range interaction within the chromatin domain determines regulatory patterns in porcine skeletal muscle.
    Article Snippet: .. LUC-ENH and LUC-CON plasmids were constructed by cloning the purified enhancer and control sequence amplified from pig genomic DNA to the MfeI (NEB) and SalI (NEB) restriction enzyme sites of STARR-seq luciferase validation vector (Addgene). .. LUC-ENH, LUC-CON and plasmid without inserted fragments (named LUCMOCK) were co-transfected with pRL-TK plasmid (BNCC) into mouse C2C12 cells (ATCC) and pig IPEC-J2 cells (BNCC) and PK-15 cells (ATCC), respectively.

    Article Title: Glucocorticoids unmask silent non-coding genetic risk variants for common diseases
    Article Snippet: .. To validate selected STARR-seq signals with clinical significance, we conducted luciferase reporter gene assays using the STARR-seq luciferase validation vector (Addgene #9927). .. The plasmid was digested with restriction enzymes BamHI-HF® (Cat#: R3136S, NEB) and SspI-HF® (Cat#: R3132S, NEB).

    Plasmid Preparation:

    Article Title: Long-range interaction within the chromatin domain determines regulatory patterns in porcine skeletal muscle.
    Article Snippet: .. LUC-ENH and LUC-CON plasmids were constructed by cloning the purified enhancer and control sequence amplified from pig genomic DNA to the MfeI (NEB) and SalI (NEB) restriction enzyme sites of STARR-seq luciferase validation vector (Addgene). .. LUC-ENH, LUC-CON and plasmid without inserted fragments (named LUCMOCK) were co-transfected with pRL-TK plasmid (BNCC) into mouse C2C12 cells (ATCC) and pig IPEC-J2 cells (BNCC) and PK-15 cells (ATCC), respectively.

    Article Title: Widespread Long-range Cis-Regulatory Elements in the Maize Genome
    Article Snippet: .. The STARR-seq plasmid sequence and additional information can be found at Addgene, deposit number 117379 ( https://www.addgene.org/117379/ ), where it is available for purchase. .. Competing Interests Robert J Schmitz and Xiaoyu Zhang are co-founders of REquest Genomics, LLC, a company that provides epigenomics services.

    Article Title: Widespread Long-range Cis-Regulatory Elements in the Maize Genome
    Article Snippet: .. Our STARR-seq plasmid sequence and additional information can be found at Addgene, deposit number 117379 ( https://www.addgene.org/117379/ ). .. The genomic DNA input for the STARR-seq assay was a ~150 kb bacterial artifical chromosome CH201-136H12 ( https://www.maizegdb.org/data_center/bac?id=613738 ) and an ATAC-seq library derived from maize second leaves.

    Reporter Assay:

    Article Title: Identification of ALK in Thinness.
    Article Snippet: .. Enhancer (luciferase reporter) assay 5x105 SH-SY5Y cells (Sigma #94030304) were electroporated via Maxcyte STX (Cat No. GOC1) with the ‘‘luciferase reporter vector’’ (Addgene ID #99297) utilizing the ORI as a core promoter (Muerdter et al., 2018) comprising either the putative identified enhancer region spanning the ALK indel rs568057364 or a negative control (Addgene ID #99315) together with a Renilla control vector (Promega # E2261) in a ratio of 10 to 1. ..

    Negative Control:

    Article Title: Identification of ALK in Thinness.
    Article Snippet: .. Enhancer (luciferase reporter) assay 5x105 SH-SY5Y cells (Sigma #94030304) were electroporated via Maxcyte STX (Cat No. GOC1) with the ‘‘luciferase reporter vector’’ (Addgene ID #99297) utilizing the ORI as a core promoter (Muerdter et al., 2018) comprising either the putative identified enhancer region spanning the ALK indel rs568057364 or a negative control (Addgene ID #99315) together with a Renilla control vector (Promega # E2261) in a ratio of 10 to 1. ..

    other:

    Article Title: Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma
    Article Snippet: We modified the NFR195B clone via site-directed mutagenesis (Q5 SDM kit E0554S; NEB) to delete the indicated OCT2-binding motif (“TTTGCAT”) and to generate the patientderived mutant allele from DLBCL 14-35632 (hg38 chr8:128172453_ T>C/chr8:128172455_G>GA).



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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