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starr seq vector  (Addgene inc)


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    Addgene inc starr seq 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
    Starr Seq Vector, supplied by Addgene inc, used in various techniques. Bioz Stars score: 95/100, based on 65 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/starr+seq+vector/hSTARR-seq_ORI+vector+(Plasmid+%2399296)/pmc12879379-317-20-23
    Average 95 stars, based on 65 article reviews
    starr seq vector - by Bioz Stars, 2026-11
    95/100 stars

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    1) Product Images from "Identification of novel DNA sequence motifs that modulate transcription in T cells"

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

    Journal: BMC Genomics

    doi: 10.1186/s12864-025-12425-9

    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
    Figure Legend 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

    Techniques Used: Sequencing, Activity Assay

    Related Articles

    Plasmid Preparation:

    Article Title: Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans
    Article Snippet: .. hSTARR-seq ORI vector , Addgene , RRID: Addgene 99296. ..

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

    Article Title: Multimodal Integration of Genomic Data Reveals Regulatory Mechanisms at the Polycystic Ovary Syndrome (PCOS)-Associated 12q13.2 Locus
    Article Snippet: .. The STARR-seq ORI vector (Addgene #99296) was linearized with AgeI/SalI, size-confirmed (~3.6 kb), and purified. .. Adapted inserts were assembled into the vector using NEBuilder HiFi, ethanol-precipitated, and transformed into E. cloni 10G SUPREME cells by electroporation.

    Article Title: Quantifying the impact of genetic mutations on enhancer dynamics.
    Article Snippet: All purification steps were performed with Ampure XP beads (catalog #A63881, Beckman Coulter, USA), using bead-to-sample volume ratio of 1.8× (adjusted for 500 bp fragments). .. The final amplified insert pool was purified twice and eluted in 40 μL, yielding concentrations >25 ng/μL and 260/280 and 260/230 ratios of 1.8 and 2.2, respectively, indicating high-quality DNA. (C) STARR-seq plasmid library cloning The human STARR-seq vector (addgene #99296) containing the ORI sequence80 was digested with restriction enzymes SalI-HF (catalog #R3138S, New England Biolabs, MA, USA) and AgeI-HF (catalog #R3552S, New England Biolabs, MA, USA), as previously described.22,24 We performed 24 independent digestion reactions with 1 μg of vector per reaction. ..

    Article Title: Identification of novel DNA sequence motifs that modulate transcription in T cells.
    Article Snippet: The sequences were then flanked with AgeI and SalI restriction sites to facilitate 589 cloning into the STARR-seq vector and ordered as a gene segment using TWIST Biosciences (San Francisco, 590 USA). .. After designing the library, the oligonucleotide 595 sequences were flanked by AgeI and SalI restriction sites to facilitate cloning into the STARR-seq vector 596 (hSTARR-seq_ORI, Addgene #99296) and the necessary priming and Illumina adapter sequences were 597 added to enable sequencing (Supplemental Table S3). ..

    Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA hSTARR-seq_ORI vector Muerdter et al. 76 Addgene Cat# 99296 pGL4.23[luc2/minP] vector Promega Cat# E8411 Software and algorithms Cell Ranger-ARC 10× Genomics v2.0.0 ArchR Granja et al. 77 v1.02 Seurat Stuart et al. 78 v3.1.5 Harmony Korsunsky et al. 79 v1.0 MACS2 Feng et al. 80 v2.2.9.1 Trimmomatic Bolger et al. 81 v0.39 Bowtie2 Langmead et al. 82 v2.3.4.1 SAMtools Li et al. 83 v1.16.1 HiC-Pro Servant et al. 84 v2.11.0 Juicer Rao et al. 85 v1.8.9 Juicebox Durand et al. 86 v1.11.08 Activity-by-Contact Fulco et al. 21 v1.1.2 LDlinkR Myers et al. 87 v1.2.0 FLASH Mago� c et al. 88 v1.2.11 BWA-MEM Li et al. 89 v0.7.12 DESeq2 Anders et al. 90 v1.26.0 mpra Myint et al. 91 v1.20.0 ChromBPNet Pampari et al. 57 v0.1.3 TF-MoDISco Shrikumar et al. 92 v0.5.6.5 Logomaker Tareen et al. 93 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Oligo(dT) Dynabeads Invitrogen Cat# 61002 RNAClean XP beads Beckman Coulter Cat# A63987 AMPure XP beads Beckman Coulter Cat# A63880 Cell Reports 45, 116814, January 27, 2026 17 18 h until collection with 10% complement competent human serum (S1-LITER, EMD Millipore), a source of activated complement factors. ..

    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.

    Cloning:

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

    Article Title: Quantifying the impact of genetic mutations on enhancer dynamics.
    Article Snippet: All purification steps were performed with Ampure XP beads (catalog #A63881, Beckman Coulter, USA), using bead-to-sample volume ratio of 1.8× (adjusted for 500 bp fragments). .. The final amplified insert pool was purified twice and eluted in 40 μL, yielding concentrations >25 ng/μL and 260/280 and 260/230 ratios of 1.8 and 2.2, respectively, indicating high-quality DNA. (C) STARR-seq plasmid library cloning The human STARR-seq vector (addgene #99296) containing the ORI sequence80 was digested with restriction enzymes SalI-HF (catalog #R3138S, New England Biolabs, MA, USA) and AgeI-HF (catalog #R3552S, New England Biolabs, MA, USA), as previously described.22,24 We performed 24 independent digestion reactions with 1 μg of vector per reaction. ..

    Article Title: Identification of novel DNA sequence motifs that modulate transcription in T cells.
    Article Snippet: The sequences were then flanked with AgeI and SalI restriction sites to facilitate 589 cloning into the STARR-seq vector and ordered as a gene segment using TWIST Biosciences (San Francisco, 590 USA). .. After designing the library, the oligonucleotide 595 sequences were flanked by AgeI and SalI restriction sites to facilitate cloning into the STARR-seq vector 596 (hSTARR-seq_ORI, Addgene #99296) and the necessary priming and Illumina adapter sequences were 597 added to enable sequencing (Supplemental Table S3). ..

    Sequencing:

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

    Article Title: Identification of novel DNA sequence motifs that modulate transcription in T cells.
    Article Snippet: The sequences were then flanked with AgeI and SalI restriction sites to facilitate 589 cloning into the STARR-seq vector and ordered as a gene segment using TWIST Biosciences (San Francisco, 590 USA). .. After designing the library, the oligonucleotide 595 sequences were flanked by AgeI and SalI restriction sites to facilitate cloning into the STARR-seq vector 596 (hSTARR-seq_ORI, Addgene #99296) and the necessary priming and Illumina adapter sequences were 597 added to enable sequencing (Supplemental Table S3). ..

    Purification:

    Article Title: Multimodal Integration of Genomic Data Reveals Regulatory Mechanisms at the Polycystic Ovary Syndrome (PCOS)-Associated 12q13.2 Locus
    Article Snippet: .. The STARR-seq ORI vector (Addgene #99296) was linearized with AgeI/SalI, size-confirmed (~3.6 kb), and purified. .. Adapted inserts were assembled into the vector using NEBuilder HiFi, ethanol-precipitated, and transformed into E. cloni 10G SUPREME cells by electroporation.

    Article Title: Quantifying the impact of genetic mutations on enhancer dynamics.
    Article Snippet: All purification steps were performed with Ampure XP beads (catalog #A63881, Beckman Coulter, USA), using bead-to-sample volume ratio of 1.8× (adjusted for 500 bp fragments). .. The final amplified insert pool was purified twice and eluted in 40 μL, yielding concentrations >25 ng/μL and 260/280 and 260/230 ratios of 1.8 and 2.2, respectively, indicating high-quality DNA. (C) STARR-seq plasmid library cloning The human STARR-seq vector (addgene #99296) containing the ORI sequence80 was digested with restriction enzymes SalI-HF (catalog #R3138S, New England Biolabs, MA, USA) and AgeI-HF (catalog #R3552S, New England Biolabs, MA, USA), as previously described.22,24 We performed 24 independent digestion reactions with 1 μg of vector per reaction. ..

    Amplification:

    Article Title: Quantifying the impact of genetic mutations on enhancer dynamics.
    Article Snippet: All purification steps were performed with Ampure XP beads (catalog #A63881, Beckman Coulter, USA), using bead-to-sample volume ratio of 1.8× (adjusted for 500 bp fragments). .. The final amplified insert pool was purified twice and eluted in 40 μL, yielding concentrations >25 ng/μL and 260/280 and 260/230 ratios of 1.8 and 2.2, respectively, indicating high-quality DNA. (C) STARR-seq plasmid library cloning The human STARR-seq vector (addgene #99296) containing the ORI sequence80 was digested with restriction enzymes SalI-HF (catalog #R3138S, New England Biolabs, MA, USA) and AgeI-HF (catalog #R3552S, New England Biolabs, MA, USA), as previously described.22,24 We performed 24 independent digestion reactions with 1 μg of vector per reaction. ..

    Recombinant:

    Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA hSTARR-seq_ORI vector Muerdter et al. 76 Addgene Cat# 99296 pGL4.23[luc2/minP] vector Promega Cat# E8411 Software and algorithms Cell Ranger-ARC 10× Genomics v2.0.0 ArchR Granja et al. 77 v1.02 Seurat Stuart et al. 78 v3.1.5 Harmony Korsunsky et al. 79 v1.0 MACS2 Feng et al. 80 v2.2.9.1 Trimmomatic Bolger et al. 81 v0.39 Bowtie2 Langmead et al. 82 v2.3.4.1 SAMtools Li et al. 83 v1.16.1 HiC-Pro Servant et al. 84 v2.11.0 Juicer Rao et al. 85 v1.8.9 Juicebox Durand et al. 86 v1.11.08 Activity-by-Contact Fulco et al. 21 v1.1.2 LDlinkR Myers et al. 87 v1.2.0 FLASH Mago� c et al. 88 v1.2.11 BWA-MEM Li et al. 89 v0.7.12 DESeq2 Anders et al. 90 v1.26.0 mpra Myint et al. 91 v1.20.0 ChromBPNet Pampari et al. 57 v0.1.3 TF-MoDISco Shrikumar et al. 92 v0.5.6.5 Logomaker Tareen et al. 93 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Oligo(dT) Dynabeads Invitrogen Cat# 61002 RNAClean XP beads Beckman Coulter Cat# A63987 AMPure XP beads Beckman Coulter Cat# A63880 Cell Reports 45, 116814, January 27, 2026 17 18 h until collection with 10% complement competent human serum (S1-LITER, EMD Millipore), a source of activated complement factors. ..

    Software:

    Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA hSTARR-seq_ORI vector Muerdter et al. 76 Addgene Cat# 99296 pGL4.23[luc2/minP] vector Promega Cat# E8411 Software and algorithms Cell Ranger-ARC 10× Genomics v2.0.0 ArchR Granja et al. 77 v1.02 Seurat Stuart et al. 78 v3.1.5 Harmony Korsunsky et al. 79 v1.0 MACS2 Feng et al. 80 v2.2.9.1 Trimmomatic Bolger et al. 81 v0.39 Bowtie2 Langmead et al. 82 v2.3.4.1 SAMtools Li et al. 83 v1.16.1 HiC-Pro Servant et al. 84 v2.11.0 Juicer Rao et al. 85 v1.8.9 Juicebox Durand et al. 86 v1.11.08 Activity-by-Contact Fulco et al. 21 v1.1.2 LDlinkR Myers et al. 87 v1.2.0 FLASH Mago� c et al. 88 v1.2.11 BWA-MEM Li et al. 89 v0.7.12 DESeq2 Anders et al. 90 v1.26.0 mpra Myint et al. 91 v1.20.0 ChromBPNet Pampari et al. 57 v0.1.3 TF-MoDISco Shrikumar et al. 92 v0.5.6.5 Logomaker Tareen et al. 93 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Oligo(dT) Dynabeads Invitrogen Cat# 61002 RNAClean XP beads Beckman Coulter Cat# A63987 AMPure XP beads Beckman Coulter Cat# A63880 Cell Reports 45, 116814, January 27, 2026 17 18 h until collection with 10% complement competent human serum (S1-LITER, EMD Millipore), a source of activated complement factors. ..

    Activity Assay:

    Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA hSTARR-seq_ORI vector Muerdter et al. 76 Addgene Cat# 99296 pGL4.23[luc2/minP] vector Promega Cat# E8411 Software and algorithms Cell Ranger-ARC 10× Genomics v2.0.0 ArchR Granja et al. 77 v1.02 Seurat Stuart et al. 78 v3.1.5 Harmony Korsunsky et al. 79 v1.0 MACS2 Feng et al. 80 v2.2.9.1 Trimmomatic Bolger et al. 81 v0.39 Bowtie2 Langmead et al. 82 v2.3.4.1 SAMtools Li et al. 83 v1.16.1 HiC-Pro Servant et al. 84 v2.11.0 Juicer Rao et al. 85 v1.8.9 Juicebox Durand et al. 86 v1.11.08 Activity-by-Contact Fulco et al. 21 v1.1.2 LDlinkR Myers et al. 87 v1.2.0 FLASH Mago� c et al. 88 v1.2.11 BWA-MEM Li et al. 89 v0.7.12 DESeq2 Anders et al. 90 v1.26.0 mpra Myint et al. 91 v1.20.0 ChromBPNet Pampari et al. 57 v0.1.3 TF-MoDISco Shrikumar et al. 92 v0.5.6.5 Logomaker Tareen et al. 93 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Oligo(dT) Dynabeads Invitrogen Cat# 61002 RNAClean XP beads Beckman Coulter Cat# A63987 AMPure XP beads Beckman Coulter Cat# A63880 Cell Reports 45, 116814, January 27, 2026 17 18 h until collection with 10% complement competent human serum (S1-LITER, EMD Millipore), a source of activated complement factors. ..



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    Addgene inc starr 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
    Starr 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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    starr seq backbone  (Addgene inc)
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    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/starr+seq+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, 2026-11
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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