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Addgene inc open reading frame orf
Open Reading Frame Orf, supplied by Addgene inc, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/open reading frame orf/product/Addgene inc
Average 92 stars, based on 2 article reviews
Price from $9.99 to $1999.99
open reading frame orf - by Bioz Stars, 2020-09
92/100 stars

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Plasmid Preparation:

Article Title: Restoration of tumour-growth suppression in vivo via systemic nanoparticle-mediated delivery of PTEN mRNA
Article Snippet: .. Vector carrying open-reading frame (ORF) of PTEN was a gift from William Sellers (pSG5L HA PTEN wt; Addgene#10750). .. The vector was linearized by ApaI/EcoRI digestion and purified.

Article Title: Quantitative Assessment of RNA-Protein Interactions with High Throughput Sequencing - RNA Affinity Profiling (HiTS-RAP)
Article Snippet: .. DNA template encoding the RNA(s) of interest mOrange pHis-// plasmid (Addgene, cat. no. 53340) mOrange pHis-// plasmid containing open-reading frame (ORF) of protein of interest Tus pGST-// plasmid (Addgene, cat. no. 53305) BL21-CodonPlus(DE3)-RIPL Competent cells (Agilent Technologies, cat. no. 230280) dNTPs (Life Technologies, cat. no. 10297-117) rNTPs (Sigma-Aldrich, cat. nos. .. A7699, G8877, U6625, and C1506) ColorpHast pH Strips (EMD Millipore, cat. no. ) Diethyl pyrocarbonate (DEPC) (Sigma-Aldrich, cat. no. 40718) CAUTION: DEPC is a suspected carcinogen.

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  • 88
    Addgene inc ccnd1 open reading frame
    Comparison of WIT medium containing EGF to WIT medium containing amphiregulin and neuregulin. Human mammary epithelial cells were infected with vectors expressing TERT , BMI1 , <t>CCND1</t> and MYC. (A) Western blots showing that the transgenes are expressed. The cells in medium containing amphiregulin and neuregulin (svWIT) have luminal characteristics. The cells in medium containing EGF (pWIT) have stronger phosphorylation of EGFR. (B) Photomicrographs showing that cells in pWIT are a mixture of spindle shaped and rounder cells, whereas cells in svWIT have a more uniform cobblestone appearance. Scale bars 250 μm. (C) Flow cytometry shows that cells in svWIT have a putative luminal progenitor phenotype (CD49+/EPCAM+) whereas cells in pWIT are a mixture of putative luminal progenitors and myoepithelial cells. The quadrants were defined by the isotype controls.
    Ccnd1 Open Reading Frame, supplied by Addgene inc, used in various techniques. Bioz Stars score: 88/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 88 stars, based on 9 article reviews
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    90
    Addgene inc notch1 icd orf
    Transcriptional Programs Related to Slow Proliferation and Stemness are Enriched in GSC8 Persisters (A) Heatmap shows expression profiles of the 4,084 most variably expressed genes across GSC8 naïve, GSC8 12d , and GSC8 Per . K-means clustering was performed to distinguish sets of genes with coherent patterns of expression across the time course of dasatinib treatment. Data was generated from three biological replicates of separately derived GSC8 12d and GSC8 Per cultures. Color represents z-scores of gene expression across rows. (B) Heatmap shows average changes in gene expression of clusters 1–6 in GSC8, GSC26 and CW1691 after 12-day treatment with gefinitib and dasatinib, respectively, compared to corresponding untreated control. Similar trends of gene expression change are evident in GSC8, GSC26 and CW1691 persisters. Color represents log2(fold-change) gene expression, where the scale ranges from the minimum to maximum value observed in GSC26 12d or CW1691 12d . (C) Gene set enrichment analysis (GSEA) shows enrichment of a cell cycle meta-signature (upper panel), gene sets related to qNSCs (middle panels), and Sox2 + medulloblastoma cells (lower panel) across naïve and persister states for GSC8 and GSC26. The cell cycle gene signature is negatively enriched, while the quiescence gene signatures are positively enriched upon drug treatment. (D) Barplots show the expression levels (reads per kilobase per million mapped reads (RPKM), y-axis) of SOX2, SOX4, OLIG2, NFIA, DLL1, <t>NOTCH1,</t> KDM5A, KDM5B and KDM6B in normal human brain (GTEx), GSC8 naïve, GSC8 12d , GSC26 naïve, GSC26 12d , CW1691 naïve, and CW1691 12d . Most genes are upregulated in drug-treated cells. Error bars represent s.e.m. (E) Barplot shows the fraction of cells (y-axis) CD133 + or CD15 + by flow cytometry. GSC8 Per display significantly increased positivity for CD133 and CD15 in comparison to GSC8 naïve (Student’s t -test; * P
    Notch1 Icd Orf, supplied by Addgene inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Addgene inc sgrnas
    GREP1 regulates GDF15. a) Cytokine profiling in HEK293T cells with transient ectopic GREP1 or GFP overexpression, ZR-75-1 cells with stable GREP1 knockout, or <t>HDQP1</t> cells with stable GREP1 knockout. The change in signal abundance was calculated for each control/GREP1 pair. To rank cytokines, the average of the absolute values for the individual signal changes was plotted. b) GDF15 abundance by ELISA in ZR-75-1 and CAMA-1 cells overexpressing a GREP1 or GFP cDNA plasmid. c) Spearman’s rho for GREP1 expression correlation with GDF15, EMILIN2, or FN1 in the indicated TCGA datasets. d) Spearman’s p value for the GREP1 correlation coefficient for GREP1 correlation with GDF15, EMILIN2, or FN1 in the indicated TCGA datasets. e-g) Recombinant GDF15 partially rescues GREP1 knockout. CAMA-1, ZR-75-1 or T47D Cas9 cells were infected with the indicated <t>sgRNAs.</t> 24 hours after infection, cells were treated with vehicle control or increasing concentration of recombinant human GDF15 as shown. Relative abundance was measured 7 days after infection. All error bars represent standard deviation.
    Sgrnas, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 310 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Addgene inc emcv ires sequence
    A multicolor biosensor to compare Cap and <t>IRES</t> translation at the single-molecule level in living cells. (A) Plasmid encodes KDM5B with an N-terminal 10xFLAG SM tag under Cap-dependent translation initiation and Kif18b with an N-terminal 24xSuntag under IRES-mediated translation initiation. Between KDM5B and SunTag is encoded the full <t>EMCV</t> IRES element. Encoded in the 3’ UTR are 24xMS2 stem loops. (B) Schematic of the system. RNA (red) is marked by MCP-Halo labeled with JF646 that binds to repeated MS2 stem loops in the 3’ UTR. Cap-dependent protein reporter (green) is labeled by anti-FLAG Fab conjugated to Cy3 that binds the 10× FLAG peptide epitopes in the N-terminus. IRES-mediated protein reporter (blue) is labeled by a GCN4 scFv fused to a GFP that binds the 24× SunTag peptide epitopes. (C) Representative cell imaged 6 hours after plasmid and probe loading. Different colored boxes within the cell illustrate different types of translation spots seen within a single cell. Example co-moving spots to right of cell. I – non-translating mRNA (red). II – single mRNA translating Cap Only (yellow). III – single mRNA translating IRES Only (purple). IV – single mRNA translating in a Cap and IRES manner (gray). (D) Quantification of species percentages out of total mRNA for both the Original Tag and the noIRES control. Each point represents the percent of that species in a cell. The p-values are based on a two-tailed Mann-Whitney test: *p
    Emcv Ires Sequence, supplied by Addgene inc, used in various techniques. Bioz Stars score: 88/100, based on 0 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Comparison of WIT medium containing EGF to WIT medium containing amphiregulin and neuregulin. Human mammary epithelial cells were infected with vectors expressing TERT , BMI1 , CCND1 and MYC. (A) Western blots showing that the transgenes are expressed. The cells in medium containing amphiregulin and neuregulin (svWIT) have luminal characteristics. The cells in medium containing EGF (pWIT) have stronger phosphorylation of EGFR. (B) Photomicrographs showing that cells in pWIT are a mixture of spindle shaped and rounder cells, whereas cells in svWIT have a more uniform cobblestone appearance. Scale bars 250 μm. (C) Flow cytometry shows that cells in svWIT have a putative luminal progenitor phenotype (CD49+/EPCAM+) whereas cells in pWIT are a mixture of putative luminal progenitors and myoepithelial cells. The quadrants were defined by the isotype controls.

    Journal: Breast Cancer Research : BCR

    Article Title: Humanization of the mouse mammary gland by replacement of the luminal layer with genetically engineered preneoplastic human cells

    doi: 10.1186/s13058-014-0504-9

    Figure Lengend Snippet: Comparison of WIT medium containing EGF to WIT medium containing amphiregulin and neuregulin. Human mammary epithelial cells were infected with vectors expressing TERT , BMI1 , CCND1 and MYC. (A) Western blots showing that the transgenes are expressed. The cells in medium containing amphiregulin and neuregulin (svWIT) have luminal characteristics. The cells in medium containing EGF (pWIT) have stronger phosphorylation of EGFR. (B) Photomicrographs showing that cells in pWIT are a mixture of spindle shaped and rounder cells, whereas cells in svWIT have a more uniform cobblestone appearance. Scale bars 250 μm. (C) Flow cytometry shows that cells in svWIT have a putative luminal progenitor phenotype (CD49+/EPCAM+) whereas cells in pWIT are a mixture of putative luminal progenitors and myoepithelial cells. The quadrants were defined by the isotype controls.

    Article Snippet: The vector expressing CCND1 and neomycin phosphotransferase (npt ) (pSV31) was constructed by Gateway cloning of the CCND1 open reading frame from pENTR-CCND1 (PlasmID HsCD00001252) into pLenti PGK Neo DEST (Addgene plasmid 19067).

    Techniques: Infection, Expressing, Western Blot, Flow Cytometry, Cytometry

    Transcriptional Programs Related to Slow Proliferation and Stemness are Enriched in GSC8 Persisters (A) Heatmap shows expression profiles of the 4,084 most variably expressed genes across GSC8 naïve, GSC8 12d , and GSC8 Per . K-means clustering was performed to distinguish sets of genes with coherent patterns of expression across the time course of dasatinib treatment. Data was generated from three biological replicates of separately derived GSC8 12d and GSC8 Per cultures. Color represents z-scores of gene expression across rows. (B) Heatmap shows average changes in gene expression of clusters 1–6 in GSC8, GSC26 and CW1691 after 12-day treatment with gefinitib and dasatinib, respectively, compared to corresponding untreated control. Similar trends of gene expression change are evident in GSC8, GSC26 and CW1691 persisters. Color represents log2(fold-change) gene expression, where the scale ranges from the minimum to maximum value observed in GSC26 12d or CW1691 12d . (C) Gene set enrichment analysis (GSEA) shows enrichment of a cell cycle meta-signature (upper panel), gene sets related to qNSCs (middle panels), and Sox2 + medulloblastoma cells (lower panel) across naïve and persister states for GSC8 and GSC26. The cell cycle gene signature is negatively enriched, while the quiescence gene signatures are positively enriched upon drug treatment. (D) Barplots show the expression levels (reads per kilobase per million mapped reads (RPKM), y-axis) of SOX2, SOX4, OLIG2, NFIA, DLL1, NOTCH1, KDM5A, KDM5B and KDM6B in normal human brain (GTEx), GSC8 naïve, GSC8 12d , GSC26 naïve, GSC26 12d , CW1691 naïve, and CW1691 12d . Most genes are upregulated in drug-treated cells. Error bars represent s.e.m. (E) Barplot shows the fraction of cells (y-axis) CD133 + or CD15 + by flow cytometry. GSC8 Per display significantly increased positivity for CD133 and CD15 in comparison to GSC8 naïve (Student’s t -test; * P

    Journal: Cell stem cell

    Article Title: Adaptive chromatin remodeling drives glioblastoma stem cell plasticity and drug tolerance

    doi: 10.1016/j.stem.2016.11.003

    Figure Lengend Snippet: Transcriptional Programs Related to Slow Proliferation and Stemness are Enriched in GSC8 Persisters (A) Heatmap shows expression profiles of the 4,084 most variably expressed genes across GSC8 naïve, GSC8 12d , and GSC8 Per . K-means clustering was performed to distinguish sets of genes with coherent patterns of expression across the time course of dasatinib treatment. Data was generated from three biological replicates of separately derived GSC8 12d and GSC8 Per cultures. Color represents z-scores of gene expression across rows. (B) Heatmap shows average changes in gene expression of clusters 1–6 in GSC8, GSC26 and CW1691 after 12-day treatment with gefinitib and dasatinib, respectively, compared to corresponding untreated control. Similar trends of gene expression change are evident in GSC8, GSC26 and CW1691 persisters. Color represents log2(fold-change) gene expression, where the scale ranges from the minimum to maximum value observed in GSC26 12d or CW1691 12d . (C) Gene set enrichment analysis (GSEA) shows enrichment of a cell cycle meta-signature (upper panel), gene sets related to qNSCs (middle panels), and Sox2 + medulloblastoma cells (lower panel) across naïve and persister states for GSC8 and GSC26. The cell cycle gene signature is negatively enriched, while the quiescence gene signatures are positively enriched upon drug treatment. (D) Barplots show the expression levels (reads per kilobase per million mapped reads (RPKM), y-axis) of SOX2, SOX4, OLIG2, NFIA, DLL1, NOTCH1, KDM5A, KDM5B and KDM6B in normal human brain (GTEx), GSC8 naïve, GSC8 12d , GSC26 naïve, GSC26 12d , CW1691 naïve, and CW1691 12d . Most genes are upregulated in drug-treated cells. Error bars represent s.e.m. (E) Barplot shows the fraction of cells (y-axis) CD133 + or CD15 + by flow cytometry. GSC8 Per display significantly increased positivity for CD133 and CD15 in comparison to GSC8 naïve (Student’s t -test; * P

    Article Snippet: Notch1 ICD ORF was PCR-amplified from Notch1 intracellular domain-pcw107 (Addgene, plasmid # 64621) using primers containing flanking Gateway attB sites and was subcloned into p-DONR221 and pIND20. dnMAML-GFP ORF was PCR-amplified from MigR1-dnMAML ( ) using primers containing flanking Gateway attB sites and was subcloned into p-DONR221 and pIND20.

    Techniques: Expressing, Generated, Derivative Assay, Flow Cytometry

    GREP1 regulates GDF15. a) Cytokine profiling in HEK293T cells with transient ectopic GREP1 or GFP overexpression, ZR-75-1 cells with stable GREP1 knockout, or HDQP1 cells with stable GREP1 knockout. The change in signal abundance was calculated for each control/GREP1 pair. To rank cytokines, the average of the absolute values for the individual signal changes was plotted. b) GDF15 abundance by ELISA in ZR-75-1 and CAMA-1 cells overexpressing a GREP1 or GFP cDNA plasmid. c) Spearman’s rho for GREP1 expression correlation with GDF15, EMILIN2, or FN1 in the indicated TCGA datasets. d) Spearman’s p value for the GREP1 correlation coefficient for GREP1 correlation with GDF15, EMILIN2, or FN1 in the indicated TCGA datasets. e-g) Recombinant GDF15 partially rescues GREP1 knockout. CAMA-1, ZR-75-1 or T47D Cas9 cells were infected with the indicated sgRNAs. 24 hours after infection, cells were treated with vehicle control or increasing concentration of recombinant human GDF15 as shown. Relative abundance was measured 7 days after infection. All error bars represent standard deviation.

    Journal: bioRxiv

    Article Title: Non-canonical open reading frames encode functional proteins essential for cancer cell survival

    doi: 10.1101/2020.03.10.981001

    Figure Lengend Snippet: GREP1 regulates GDF15. a) Cytokine profiling in HEK293T cells with transient ectopic GREP1 or GFP overexpression, ZR-75-1 cells with stable GREP1 knockout, or HDQP1 cells with stable GREP1 knockout. The change in signal abundance was calculated for each control/GREP1 pair. To rank cytokines, the average of the absolute values for the individual signal changes was plotted. b) GDF15 abundance by ELISA in ZR-75-1 and CAMA-1 cells overexpressing a GREP1 or GFP cDNA plasmid. c) Spearman’s rho for GREP1 expression correlation with GDF15, EMILIN2, or FN1 in the indicated TCGA datasets. d) Spearman’s p value for the GREP1 correlation coefficient for GREP1 correlation with GDF15, EMILIN2, or FN1 in the indicated TCGA datasets. e-g) Recombinant GDF15 partially rescues GREP1 knockout. CAMA-1, ZR-75-1 or T47D Cas9 cells were infected with the indicated sgRNAs. 24 hours after infection, cells were treated with vehicle control or increasing concentration of recombinant human GDF15 as shown. Relative abundance was measured 7 days after infection. All error bars represent standard deviation.

    Article Snippet: For stable knockout cell lines, ZR-75-1 Cas9 and HDQP1 Cas9 expressing cells were infected with lentivirus for the indicated sgRNAs which had been cloned into the LentiGuide-Puro plasmid (plasmid #52963, Addgene) with 4ug/mL of polybrene.

    Techniques: Over Expression, Knock-Out, Enzyme-linked Immunosorbent Assay, Plasmid Preparation, Expressing, Recombinant, Infection, Concentration Assay, Standard Deviation

    A multicolor biosensor to compare Cap and IRES translation at the single-molecule level in living cells. (A) Plasmid encodes KDM5B with an N-terminal 10xFLAG SM tag under Cap-dependent translation initiation and Kif18b with an N-terminal 24xSuntag under IRES-mediated translation initiation. Between KDM5B and SunTag is encoded the full EMCV IRES element. Encoded in the 3’ UTR are 24xMS2 stem loops. (B) Schematic of the system. RNA (red) is marked by MCP-Halo labeled with JF646 that binds to repeated MS2 stem loops in the 3’ UTR. Cap-dependent protein reporter (green) is labeled by anti-FLAG Fab conjugated to Cy3 that binds the 10× FLAG peptide epitopes in the N-terminus. IRES-mediated protein reporter (blue) is labeled by a GCN4 scFv fused to a GFP that binds the 24× SunTag peptide epitopes. (C) Representative cell imaged 6 hours after plasmid and probe loading. Different colored boxes within the cell illustrate different types of translation spots seen within a single cell. Example co-moving spots to right of cell. I – non-translating mRNA (red). II – single mRNA translating Cap Only (yellow). III – single mRNA translating IRES Only (purple). IV – single mRNA translating in a Cap and IRES manner (gray). (D) Quantification of species percentages out of total mRNA for both the Original Tag and the noIRES control. Each point represents the percent of that species in a cell. The p-values are based on a two-tailed Mann-Whitney test: *p

    Journal: bioRxiv

    Article Title: Quantifying the spatiotemporal dynamics of IRES versus Cap translation with single-molecule resolution in living cells

    doi: 10.1101/2020.01.09.900829

    Figure Lengend Snippet: A multicolor biosensor to compare Cap and IRES translation at the single-molecule level in living cells. (A) Plasmid encodes KDM5B with an N-terminal 10xFLAG SM tag under Cap-dependent translation initiation and Kif18b with an N-terminal 24xSuntag under IRES-mediated translation initiation. Between KDM5B and SunTag is encoded the full EMCV IRES element. Encoded in the 3’ UTR are 24xMS2 stem loops. (B) Schematic of the system. RNA (red) is marked by MCP-Halo labeled with JF646 that binds to repeated MS2 stem loops in the 3’ UTR. Cap-dependent protein reporter (green) is labeled by anti-FLAG Fab conjugated to Cy3 that binds the 10× FLAG peptide epitopes in the N-terminus. IRES-mediated protein reporter (blue) is labeled by a GCN4 scFv fused to a GFP that binds the 24× SunTag peptide epitopes. (C) Representative cell imaged 6 hours after plasmid and probe loading. Different colored boxes within the cell illustrate different types of translation spots seen within a single cell. Example co-moving spots to right of cell. I – non-translating mRNA (red). II – single mRNA translating Cap Only (yellow). III – single mRNA translating IRES Only (purple). IV – single mRNA translating in a Cap and IRES manner (gray). (D) Quantification of species percentages out of total mRNA for both the Original Tag and the noIRES control. Each point represents the percent of that species in a cell. The p-values are based on a two-tailed Mann-Whitney test: *p

    Article Snippet: The EMCV IRES sequence was amplified by PCR from EMCV_IRES_pcDNA4TO_H2B_SunTag24x_v1 (Addgene #246719) using the following primers: 5’-CCG AAA GGT TTA AAC GCT AGC ACG TTA CTG GCC GAA-3’; 5’-TTC TTC TCC TCC AGA GCT AGC TAT TAT CAT CGT GTT TTT CAA AGG AAA-3’.

    Techniques: Plasmid Preparation, Labeling, Two Tailed Test, MANN-WHITNEY