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Addgene inc muerdter
Muerdter, supplied by Addgene inc, used in various techniques. Bioz Stars score: 95/100, based on 60 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/hstarr+seq+ori+vector/hSTARR-seq_ORI+vector+(Plasmid+%2399296)/pmc12971065-42-3-7
Average 95 stars, based on 60 article reviews
muerdter - by Bioz Stars, 2026-09
95/100 stars

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Plasmid Preparation:

Article Title: Challenges and considerations for reproducibility of STARR-seq assays
Article Snippet: 520 521 522 523 524 525 526 527 528 529 530 (1E) Vector preparation: Vector culturing 531 Use human STARR-seq vector ADDgene #99296 as reported by Muerdter and colleagues 532 (Muerdter et al. 2018). .. The hSTARR-seq_ORI vector was a gift from Alexander Stark (Addgene 533 plasmid # 99296 ; http://n2t.net/addgene:99296 ; RRID:Addgene_99296) 534 1. ..

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [ ]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [ ]. ..

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [25]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [61]. ..

Article Title: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development.
Article Snippet: potential critical enhancers and their gene regulatory networks underlying skeletal muscle development Song Zhang, Chao Wang, Shenghua Qin, Choulin Chen, Yongzhou Bao, Yuanyuan Zhang, Lingna Xu, Qingyou Liu, Yunxiang Zhao, Kui Li, Zhonglin Tang, and Yuwen Liu Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China; Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China

Article Title: Systematic functional characterization of non-coding regulatory SNPs associated with central obesity.
Article Snippet: ARTICLE Systematic functional characterization of non-coding regulatory SNPs associated with central obesity

Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration
Article Snippet: Recombinant DNA , , . .. hSTARR-seq_ORI vector , Muerdter et al. , Addgene Cat# 99296. .. pGL4.23[luc2/minP] vector , Promega , Cat# E8411.

Article Title: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq.
Article Snippet: progenitor cells using capture STARR-seq Sophia C. Gaynor-Gillett, Lijun Cheng, Manman Shi, Jason Liu, Gaoyuan Wang, Megan Spector, Qiuyu Guo, Le Qi, Mary Flaherty, Martha Wall, Ahyeon Hwang, Mengting Gu, Zhanlin Chen, Yuhang Chen, PsychENCODE Consortium, Jennifer R. Moran, Jing Zhang, Donghoon Lee, Mark Gerstein, Daniel Geschwind, and Kevin P. White Department of Biology, Cornell College, Mount Vernon, Iowa 52314, USA; Tempus Labs, Inc., Chicago, Illinois 60654, USA; Computational Biology and Bioinformatics Program, Yale University, New Haven, Connecticut 06511, USA; Discovery Biomarkers, Amgen Research, Thousand Oaks, California 91320, USA; Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA; Department of Computer Science, University of California Irvine, Irvine, California 92697, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; Department of Statistics and Data Science, Yale University, New Haven, Connecticut 06511, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA; Department of Computer Science, Yale University, New Haven, Connecticut 06511, USA; Department of Psychiatry and Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA; Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore

Modification:

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [ ]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [ ]. ..

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [25]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [61]. ..

Sequencing:

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [ ]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [ ]. ..

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [25]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [61]. ..

Binding Assay:

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [ ]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [ ]. ..

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [25]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [61]. ..

Methylation:

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [ ]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [ ]. ..

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [25]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [61]. ..

Expressing:

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [ ]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [ ]. ..

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [25]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [61]. ..

Activity Assay:

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [ ]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [ ]. ..

Article Title: HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.
Article Snippet: .. Plasmids hSTARR-seq_SCP1 vector (Addgene plasmid # 99292, RRID:Addgene_99292; listed as pTYC6 in Table S1E) and hSTARR-seq_ORI vector (Addgene plasmid # 99296, RRID:Addgene_99296; pTYC7 in Table S1E) were gifts from Alexander Stark [25]. hSTARR-seq_SCP1 was modified to generate plasmid pTYC10 by removing the SCP1 promoter sequence by BanII digestion and replacing it with a minimal mouse Alb promoter sequence, comprised of 318 nt obtained from pLIVE plasmid (cat. #MIR 5420, Mirus Inc, Madison, WI), where the Alb promoter HNF1 TF binding site was changed from GATC to AATC to prevent bacterial methylation and to enable expression of the full intrinsic activity of the Alb promoter in HDI-transfected livers [61]. ..

Amplification:

Article Title: Systematic functional characterization of non-coding regulatory SNPs associated with central obesity.
Article Snippet: ARTICLE Systematic functional characterization of non-coding regulatory SNPs associated with central obesity

Clone Assay:

Article Title: Systematic functional characterization of non-coding regulatory SNPs associated with central obesity.
Article Snippet: ARTICLE Systematic functional characterization of non-coding regulatory SNPs associated with central obesity

Article Title: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq.
Article Snippet: progenitor cells using capture STARR-seq Sophia C. Gaynor-Gillett, Lijun Cheng, Manman Shi, Jason Liu, Gaoyuan Wang, Megan Spector, Qiuyu Guo, Le Qi, Mary Flaherty, Martha Wall, Ahyeon Hwang, Mengting Gu, Zhanlin Chen, Yuhang Chen, PsychENCODE Consortium, Jennifer R. Moran, Jing Zhang, Donghoon Lee, Mark Gerstein, Daniel Geschwind, and Kevin P. White Department of Biology, Cornell College, Mount Vernon, Iowa 52314, USA; Tempus Labs, Inc., Chicago, Illinois 60654, USA; Computational Biology and Bioinformatics Program, Yale University, New Haven, Connecticut 06511, USA; Discovery Biomarkers, Amgen Research, Thousand Oaks, California 91320, USA; Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA; Department of Computer Science, University of California Irvine, Irvine, California 92697, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; Department of Statistics and Data Science, Yale University, New Haven, Connecticut 06511, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA; Department of Computer Science, Yale University, New Haven, Connecticut 06511, USA; Department of Psychiatry and Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA; Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore

Transfection:

Article Title: Systematic functional characterization of non-coding regulatory SNPs associated with central obesity.
Article Snippet: ARTICLE Systematic functional characterization of non-coding regulatory SNPs associated with central obesity

Hybridization:

Article Title: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq.
Article Snippet: progenitor cells using capture STARR-seq Sophia C. Gaynor-Gillett, Lijun Cheng, Manman Shi, Jason Liu, Gaoyuan Wang, Megan Spector, Qiuyu Guo, Le Qi, Mary Flaherty, Martha Wall, Ahyeon Hwang, Mengting Gu, Zhanlin Chen, Yuhang Chen, PsychENCODE Consortium, Jennifer R. Moran, Jing Zhang, Donghoon Lee, Mark Gerstein, Daniel Geschwind, and Kevin P. White Department of Biology, Cornell College, Mount Vernon, Iowa 52314, USA; Tempus Labs, Inc., Chicago, Illinois 60654, USA; Computational Biology and Bioinformatics Program, Yale University, New Haven, Connecticut 06511, USA; Discovery Biomarkers, Amgen Research, Thousand Oaks, California 91320, USA; Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA; Department of Computer Science, University of California Irvine, Irvine, California 92697, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; Department of Statistics and Data Science, Yale University, New Haven, Connecticut 06511, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA; Department of Computer Science, Yale University, New Haven, Connecticut 06511, USA; Department of Psychiatry and Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA; Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore



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Addgene inc age1 sal1 digested hstarr seq ori vector
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
Age1 Sal1 Digested Hstarr Seq Ori Vector, supplied by Addgene inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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age1 sal1 digested hstarr seq ori vector - by Bioz Stars, 2026-09
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95
Addgene inc starr seq backbone
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
Starr Seq Backbone, supplied by Addgene inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/hstarr+seq+ori+vector/hSTARR-seq_ORI+vector+(Plasmid+%2399296)/pm40825976-97-8-10
Average 95 stars, based on 1 article reviews
starr seq backbone - by Bioz Stars, 2026-09
95/100 stars
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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