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  • 99
    Thermo Fisher cdna cdna
    Cdna Cdna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 111 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Millipore cdna synthesis
    SeT deletion in primary murine macrophages. (A) Representative graph of the murine <t>Tnfα</t> gene locus indicating the homology ( > 70%) with the human and chimpanzee genomes, mapping of the SeT lncRNA as well as the primer utilized for generating the SeT <t>cDNA</t> (RT) and the subsequent PCR products (1–6) with the SeT cDNA as template (blue: gene exons, yellow: untranslated regions, red: intergenic regions, arrows above genes: direction of gene transcription). (B) Diagrammatic representation of the targeting construct used for the SeT -/- mouse generation. (C) Genotyping of the mutated SeT mice. Detection by RT-PCR of the deletion of 1647 bp region in genomic extracts of primary macrophages isolated from the peritoneum (TEPMs) or the bone marrow (BMDMs) of CX3CR1-Cre SeT fl/fl mice and SeT -/- BMDMs. M: MW marker, WT: wild type, M1-M3/KO: different genomic DNA samples derived from mice bearing the deleted allele in homozygosity, HET: heterozygote sample (bearing one wild type and one deleted allele for SeT ), FX: floxed alleles. D) RT-PCR reactions for the detection of the relative mRNA levels for the lncRNA SeT and Hprt1 gene transcripts (mapping of PCR products is indicated in panel A).
    Cdna Synthesis, supplied by Millipore, used in various techniques. Bioz Stars score: 96/100, based on 2592 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    GE Healthcare cdnas
    SeT deletion in primary murine macrophages. (A) Representative graph of the murine <t>Tnfα</t> gene locus indicating the homology ( > 70%) with the human and chimpanzee genomes, mapping of the SeT lncRNA as well as the primer utilized for generating the SeT <t>cDNA</t> (RT) and the subsequent PCR products (1–6) with the SeT cDNA as template (blue: gene exons, yellow: untranslated regions, red: intergenic regions, arrows above genes: direction of gene transcription). (B) Diagrammatic representation of the targeting construct used for the SeT -/- mouse generation. (C) Genotyping of the mutated SeT mice. Detection by RT-PCR of the deletion of 1647 bp region in genomic extracts of primary macrophages isolated from the peritoneum (TEPMs) or the bone marrow (BMDMs) of CX3CR1-Cre SeT fl/fl mice and SeT -/- BMDMs. M: MW marker, WT: wild type, M1-M3/KO: different genomic DNA samples derived from mice bearing the deleted allele in homozygosity, HET: heterozygote sample (bearing one wild type and one deleted allele for SeT ), FX: floxed alleles. D) RT-PCR reactions for the detection of the relative mRNA levels for the lncRNA SeT and Hprt1 gene transcripts (mapping of PCR products is indicated in panel A).
    Cdnas, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 93/100, based on 3235 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Horizon Discovery cdnas
    SeT deletion in primary murine macrophages. (A) Representative graph of the murine <t>Tnfα</t> gene locus indicating the homology ( > 70%) with the human and chimpanzee genomes, mapping of the SeT lncRNA as well as the primer utilized for generating the SeT <t>cDNA</t> (RT) and the subsequent PCR products (1–6) with the SeT cDNA as template (blue: gene exons, yellow: untranslated regions, red: intergenic regions, arrows above genes: direction of gene transcription). (B) Diagrammatic representation of the targeting construct used for the SeT -/- mouse generation. (C) Genotyping of the mutated SeT mice. Detection by RT-PCR of the deletion of 1647 bp region in genomic extracts of primary macrophages isolated from the peritoneum (TEPMs) or the bone marrow (BMDMs) of CX3CR1-Cre SeT fl/fl mice and SeT -/- BMDMs. M: MW marker, WT: wild type, M1-M3/KO: different genomic DNA samples derived from mice bearing the deleted allele in homozygosity, HET: heterozygote sample (bearing one wild type and one deleted allele for SeT ), FX: floxed alleles. D) RT-PCR reactions for the detection of the relative mRNA levels for the lncRNA SeT and Hprt1 gene transcripts (mapping of PCR products is indicated in panel A).
    Cdnas, supplied by Horizon Discovery, used in various techniques. Bioz Stars score: 92/100, based on 130 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Incyte cdnas
    Global analysis of fibroblast gene expression in response to IFN, gB, or HCMV infection. Intensity data from all of the <t>cDNAs</t> on the <t>microarrays</t> obtained at 8 and 24 h were log-transformed, and scatter plots were generated to assess differential gene expression between samples. Pair-wise similarity of gene-expression profiles was measured by the correlation coefficient; r ). The 2-h time points were omitted from this analysis because relatively few genes changed at this early time point.
    Cdnas, supplied by Incyte, used in various techniques. Bioz Stars score: 92/100, based on 63 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Promega cdnas
    Global analysis of fibroblast gene expression in response to IFN, gB, or HCMV infection. Intensity data from all of the <t>cDNAs</t> on the <t>microarrays</t> obtained at 8 and 24 h were log-transformed, and scatter plots were generated to assess differential gene expression between samples. Pair-wise similarity of gene-expression profiles was measured by the correlation coefficient; r ). The 2-h time points were omitted from this analysis because relatively few genes changed at this early time point.
    Cdnas, supplied by Promega, used in various techniques. Bioz Stars score: 94/100, based on 9326 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Thermo Fisher cdnas
    Overexpression of caspases is not sufficient to accelerate islet cell apoptosis. 832/13 and primary rat islets were untreated (no virus) or treated with recombinant adenoviruses containing <t>cDNAs</t> corresponding to human Apaf-1, human <t>caspase</t> 3, human caspase 9 or the control gene, β-galactosidase (β-gal), as indicated. 72 h post-infection, 832/13 cells ( A ) and primary rat islets ( B ) were treated with DMSO (control) or thapsigargin (100 nM or 1 μM, respectively) for 18 h. Clarified lysates were examined by immunoblot analysis. Endogenous rat (r) and overexpressed human (h) proteins are labeled accordingly. Of note, Apaf-1 and caspase 9 antibodies only detect human (overexpressed) proteins. ( C , D ) 72 h post adenoviral infection, rat islets were treated with DMSO (control) or thapsigargin (1 μM) for up to 72 h. Islet cells were stained for TUNEL, caspase 3, and insulin and counterstained with DAPI. Cells were imaged using a high content imager and analyzed using Cellomics software. ( C ) Percentages of insulin+ TUNEL+ islet cells are shown. ( D ) Comparison of the percentages of caspase 3+ (overexpressing), TUNEL+ islet cells vs. caspase 3- (non-overexpressing), TUNEL+ islet cells are shown. ( C , D ) Data represent the mean +S.E.M. of 3 independent experiments. * p ≤ 0.05 as compared to DMSO treated cells.
    Cdnas, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 66998 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Addgene inc cdnas
    Attempts to Obtain Chicken Reprogrammed Cells with Various Delivery Systems Primary chicken embryonic fibroblasts (CEFs) were infected with the pLent polycistronic lentivirus. Colonies emerged (A) and expressed GFP (B), indicating that they were infected, although they failed to be amplified. More than 50 colonies were isolated in several independent experiments. Similarly, CEFs were infected with a cocktail of individual lentiviruses carrying mouse Oct4 , <t>Sox2</t> , Klf4 , and c-Myc <t>cDNAs.</t> Compact colonies with AP-positive cells were obtained (C and D) but could not be established long term. In another attempt, CEFs were infected with pMX retroviruses carrying mouse Oct4 , Sox2 , Klf4 , and c-Myc . Morphological changes were rapidly observed (E), and colonies expanded once individually picked (F). The phenotypic changes were not stable, and cells reverted to a fibroblast phenotype (G) after four to six passages. Similarly, CEFs infected with Sendai viruses carrying human OCT4 , SOX2 , KLF4 , and c-MYC cDNAs exhibited morphological changes (H) but failed to be established and reverted to a fibroblast phenotype after a few passages. Scale bars, 50 μm.
    Cdnas, supplied by Addgene inc, used in various techniques. Bioz Stars score: 92/100, based on 1176 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Eurofins cdnas
    Attempts to Obtain Chicken Reprogrammed Cells with Various Delivery Systems Primary chicken embryonic fibroblasts (CEFs) were infected with the pLent polycistronic lentivirus. Colonies emerged (A) and expressed GFP (B), indicating that they were infected, although they failed to be amplified. More than 50 colonies were isolated in several independent experiments. Similarly, CEFs were infected with a cocktail of individual lentiviruses carrying mouse Oct4 , <t>Sox2</t> , Klf4 , and c-Myc <t>cDNAs.</t> Compact colonies with AP-positive cells were obtained (C and D) but could not be established long term. In another attempt, CEFs were infected with pMX retroviruses carrying mouse Oct4 , Sox2 , Klf4 , and c-Myc . Morphological changes were rapidly observed (E), and colonies expanded once individually picked (F). The phenotypic changes were not stable, and cells reverted to a fibroblast phenotype (G) after four to six passages. Similarly, CEFs infected with Sendai viruses carrying human OCT4 , SOX2 , KLF4 , and c-MYC cDNAs exhibited morphological changes (H) but failed to be established and reverted to a fibroblast phenotype after a few passages. Scale bars, 50 μm.
    Cdnas, supplied by Eurofins, used in various techniques. Bioz Stars score: 92/100, based on 351 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Operon Biotech cdnas
    Attempts to Obtain Chicken Reprogrammed Cells with Various Delivery Systems Primary chicken embryonic fibroblasts (CEFs) were infected with the pLent polycistronic lentivirus. Colonies emerged (A) and expressed GFP (B), indicating that they were infected, although they failed to be amplified. More than 50 colonies were isolated in several independent experiments. Similarly, CEFs were infected with a cocktail of individual lentiviruses carrying mouse Oct4 , <t>Sox2</t> , Klf4 , and c-Myc <t>cDNAs.</t> Compact colonies with AP-positive cells were obtained (C and D) but could not be established long term. In another attempt, CEFs were infected with pMX retroviruses carrying mouse Oct4 , Sox2 , Klf4 , and c-Myc . Morphological changes were rapidly observed (E), and colonies expanded once individually picked (F). The phenotypic changes were not stable, and cells reverted to a fibroblast phenotype (G) after four to six passages. Similarly, CEFs infected with Sendai viruses carrying human OCT4 , SOX2 , KLF4 , and c-MYC cDNAs exhibited morphological changes (H) but failed to be established and reverted to a fibroblast phenotype after a few passages. Scale bars, 50 μm.
    Cdnas, supplied by Operon Biotech, used in various techniques. Bioz Stars score: 92/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc cdnas
    Adapter-tRNA ligation efficiencies with a conventional method and YAMAT-seq. ( A ) Schematic representation of the adapter ligation reactions used in the conventional and YAMAT-seq methods. In the conventional method, tRNA was subjected to 3΄-adapter (3΄-AD) and 5΄-adapter (5΄-AD) ligations catalyzed by truncated Rnl2 and Rnl1, respectively, using the <t>Illumina</t> TruSeq Small RNA Sample Preparation Kit. In contrast, in the YAMAT-seq method, a Y-shaped adapter (Y-AD) is ligated to a tRNA by Rnl2. ( B ) Ligation products of synthetic human cyto tRNA AspGUC and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. The amounts of ligation products were determined based on standard curves, and ligation efficiencies were calculated as percentages of ligated tRNA versus input tRNA (set as 100%). Each data set represents the average of three independent experiments with bars showing the SD. ( C ) Ligation products of the indicated native cyto tRNAs in BT-474 total RNA and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. Each data set represents the average Ct values of three independent experiments with bars showing the SD. ( D ) Image of 8% native polyacrylamide gel electrophoresis (PAGE) of amplified <t>cDNAs</t> resulting from BT-474 total RNA sequencing by conventional and YAMAT-seq procedures. The total adapter lengths of the conventional and YAMAT-seq procedures are 118 and 140 bp, respectively. The YAMAT-seq-derived cDNAs in the designated Bands 1–3 regions were gel-purified and subjected to cloning; the identified sequences are shown in Supplementary Table S1 . The cDNAs in regions designated with gray lines are expected to contain tRNA fraction.
    Cdnas, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 3587 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    OriGene cdnas
    Adapter-tRNA ligation efficiencies with a conventional method and YAMAT-seq. ( A ) Schematic representation of the adapter ligation reactions used in the conventional and YAMAT-seq methods. In the conventional method, tRNA was subjected to 3΄-adapter (3΄-AD) and 5΄-adapter (5΄-AD) ligations catalyzed by truncated Rnl2 and Rnl1, respectively, using the <t>Illumina</t> TruSeq Small RNA Sample Preparation Kit. In contrast, in the YAMAT-seq method, a Y-shaped adapter (Y-AD) is ligated to a tRNA by Rnl2. ( B ) Ligation products of synthetic human cyto tRNA AspGUC and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. The amounts of ligation products were determined based on standard curves, and ligation efficiencies were calculated as percentages of ligated tRNA versus input tRNA (set as 100%). Each data set represents the average of three independent experiments with bars showing the SD. ( C ) Ligation products of the indicated native cyto tRNAs in BT-474 total RNA and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. Each data set represents the average Ct values of three independent experiments with bars showing the SD. ( D ) Image of 8% native polyacrylamide gel electrophoresis (PAGE) of amplified <t>cDNAs</t> resulting from BT-474 total RNA sequencing by conventional and YAMAT-seq procedures. The total adapter lengths of the conventional and YAMAT-seq procedures are 118 and 140 bp, respectively. The YAMAT-seq-derived cDNAs in the designated Bands 1–3 regions were gel-purified and subjected to cloning; the identified sequences are shown in Supplementary Table S1 . The cDNAs in regions designated with gray lines are expected to contain tRNA fraction.
    Cdnas, supplied by OriGene, used in various techniques. Bioz Stars score: 93/100, based on 818 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Unigene cdnas
    Experimental set up and overall expression profiles. (a) The time course of gene expression was determined during the response of two different fibroblast types; 2091 derived from foreskin and WI-38 derived from fetal lung. Each was treated with either the indicated GFs, epidermal growth factor (EGF), fibroblast growth factor (FGF), platelet derived growth factor (PDGF) or FBS (Serum), and three replicate time courses were run for each treatment. The layout of the samples in the other panels as well as in Figures 2-6 is as shown here. (b) Hierarchical cluster of 1,304 genes with a minimum expression change of twofold in at least 15 array experiments and with data present in at least 80% of all array samples. <t>cDNAs</t> with no known <t>Unigene</t> annotation or mapping to multiple Unigene clusters were removed. Black bars on the right indicate consistently induced genes. (c) Sub-cluster branches containing the consistently induced genes were selected and re-clustered. This set included 237 genes represented by 278 cDNA probes. (d) Consistently repressed genes were selected directly from expression data as described in Materials and methods and clustered. This set included 237 genes represented by 250 cDNA probes.
    Cdnas, supplied by Unigene, used in various techniques. Bioz Stars score: 93/100, based on 393 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    EUROIMMUN cdnas
    Experimental set up and overall expression profiles. (a) The time course of gene expression was determined during the response of two different fibroblast types; 2091 derived from foreskin and WI-38 derived from fetal lung. Each was treated with either the indicated GFs, epidermal growth factor (EGF), fibroblast growth factor (FGF), platelet derived growth factor (PDGF) or FBS (Serum), and three replicate time courses were run for each treatment. The layout of the samples in the other panels as well as in Figures 2-6 is as shown here. (b) Hierarchical cluster of 1,304 genes with a minimum expression change of twofold in at least 15 array experiments and with data present in at least 80% of all array samples. <t>cDNAs</t> with no known <t>Unigene</t> annotation or mapping to multiple Unigene clusters were removed. Black bars on the right indicate consistently induced genes. (c) Sub-cluster branches containing the consistently induced genes were selected and re-clustered. This set included 237 genes represented by 278 cDNA probes. (d) Consistently repressed genes were selected directly from expression data as described in Materials and methods and clustered. This set included 237 genes represented by 250 cDNA probes.
    Cdnas, supplied by EUROIMMUN, used in various techniques. Bioz Stars score: 92/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    SLIT2 LTD cdnas
    Experimental set up and overall expression profiles. (a) The time course of gene expression was determined during the response of two different fibroblast types; 2091 derived from foreskin and WI-38 derived from fetal lung. Each was treated with either the indicated GFs, epidermal growth factor (EGF), fibroblast growth factor (FGF), platelet derived growth factor (PDGF) or FBS (Serum), and three replicate time courses were run for each treatment. The layout of the samples in the other panels as well as in Figures 2-6 is as shown here. (b) Hierarchical cluster of 1,304 genes with a minimum expression change of twofold in at least 15 array experiments and with data present in at least 80% of all array samples. <t>cDNAs</t> with no known <t>Unigene</t> annotation or mapping to multiple Unigene clusters were removed. Black bars on the right indicate consistently induced genes. (c) Sub-cluster branches containing the consistently induced genes were selected and re-clustered. This set included 237 genes represented by 278 cDNA probes. (d) Consistently repressed genes were selected directly from expression data as described in Materials and methods and clustered. This set included 237 genes represented by 250 cDNA probes.
    Cdnas, supplied by SLIT2 LTD, used in various techniques. Bioz Stars score: 92/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cdnas/product/SLIT2 LTD
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    92
    TaKaRa cdnas
    ( A ) C-type lectin receptors (CLR) mRNA expression in adult human tissues. Quantitative real-time <t>PCR</t> analysis was performed on pre-normalized <t>cDNAs</t> derived from poly(A)-selected DNase-treated RNAs purified from pools of healthy human tissues as described in methods; ( B ) CLR mRNA expression in adult mouse tissues. Real-time PCR was performed on pooled cDNAs derived from five adult six to eight week old C57BL/6 mice as described in methods. Biological replicates were quantified in triplicates and normalized to the respective GAPDH mRNA level. The results in the table are expressed relative to the respective expression level of each transcript in spleen. In the table, red shades indicate higher and green shades indicate lower mRNA levels as compared to the respective mRNA levels in spleen. The spleen mRNA levels are illustrated in the histogram on top of the table. Data in B represents means ± SEM. * indicated statistical significance p
    Cdnas, supplied by TaKaRa, used in various techniques. Bioz Stars score: 92/100, based on 18140 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Bioneer Corporation cdnas
    ( A ) C-type lectin receptors (CLR) mRNA expression in adult human tissues. Quantitative real-time <t>PCR</t> analysis was performed on pre-normalized <t>cDNAs</t> derived from poly(A)-selected DNase-treated RNAs purified from pools of healthy human tissues as described in methods; ( B ) CLR mRNA expression in adult mouse tissues. Real-time PCR was performed on pooled cDNAs derived from five adult six to eight week old C57BL/6 mice as described in methods. Biological replicates were quantified in triplicates and normalized to the respective GAPDH mRNA level. The results in the table are expressed relative to the respective expression level of each transcript in spleen. In the table, red shades indicate higher and green shades indicate lower mRNA levels as compared to the respective mRNA levels in spleen. The spleen mRNA levels are illustrated in the histogram on top of the table. Data in B represents means ± SEM. * indicated statistical significance p
    Cdnas, supplied by Bioneer Corporation, used in various techniques. Bioz Stars score: 93/100, based on 372 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Meridian Life Science cdnas
    ( A ) C-type lectin receptors (CLR) mRNA expression in adult human tissues. Quantitative real-time <t>PCR</t> analysis was performed on pre-normalized <t>cDNAs</t> derived from poly(A)-selected DNase-treated RNAs purified from pools of healthy human tissues as described in methods; ( B ) CLR mRNA expression in adult mouse tissues. Real-time PCR was performed on pooled cDNAs derived from five adult six to eight week old C57BL/6 mice as described in methods. Biological replicates were quantified in triplicates and normalized to the respective GAPDH mRNA level. The results in the table are expressed relative to the respective expression level of each transcript in spleen. In the table, red shades indicate higher and green shades indicate lower mRNA levels as compared to the respective mRNA levels in spleen. The spleen mRNA levels are illustrated in the histogram on top of the table. Data in B represents means ± SEM. * indicated statistical significance p
    Cdnas, supplied by Meridian Life Science, used in various techniques. Bioz Stars score: 92/100, based on 365 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Mirus Bio cdnas
    ( A ) C-type lectin receptors (CLR) mRNA expression in adult human tissues. Quantitative real-time <t>PCR</t> analysis was performed on pre-normalized <t>cDNAs</t> derived from poly(A)-selected DNase-treated RNAs purified from pools of healthy human tissues as described in methods; ( B ) CLR mRNA expression in adult mouse tissues. Real-time PCR was performed on pooled cDNAs derived from five adult six to eight week old C57BL/6 mice as described in methods. Biological replicates were quantified in triplicates and normalized to the respective GAPDH mRNA level. The results in the table are expressed relative to the respective expression level of each transcript in spleen. In the table, red shades indicate higher and green shades indicate lower mRNA levels as compared to the respective mRNA levels in spleen. The spleen mRNA levels are illustrated in the histogram on top of the table. Data in B represents means ± SEM. * indicated statistical significance p
    Cdnas, supplied by Mirus Bio, used in various techniques. Bioz Stars score: 92/100, based on 114 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    R&D Systems cdnas
    ( A ) C-type lectin receptors (CLR) mRNA expression in adult human tissues. Quantitative real-time <t>PCR</t> analysis was performed on pre-normalized <t>cDNAs</t> derived from poly(A)-selected DNase-treated RNAs purified from pools of healthy human tissues as described in methods; ( B ) CLR mRNA expression in adult mouse tissues. Real-time PCR was performed on pooled cDNAs derived from five adult six to eight week old C57BL/6 mice as described in methods. Biological replicates were quantified in triplicates and normalized to the respective GAPDH mRNA level. The results in the table are expressed relative to the respective expression level of each transcript in spleen. In the table, red shades indicate higher and green shades indicate lower mRNA levels as compared to the respective mRNA levels in spleen. The spleen mRNA levels are illustrated in the histogram on top of the table. Data in B represents means ± SEM. * indicated statistical significance p
    Cdnas, supplied by R&D Systems, used in various techniques. Bioz Stars score: 92/100, based on 17 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Evrogen cdnas
    ( A ) C-type lectin receptors (CLR) mRNA expression in adult human tissues. Quantitative real-time <t>PCR</t> analysis was performed on pre-normalized <t>cDNAs</t> derived from poly(A)-selected DNase-treated RNAs purified from pools of healthy human tissues as described in methods; ( B ) CLR mRNA expression in adult mouse tissues. Real-time PCR was performed on pooled cDNAs derived from five adult six to eight week old C57BL/6 mice as described in methods. Biological replicates were quantified in triplicates and normalized to the respective GAPDH mRNA level. The results in the table are expressed relative to the respective expression level of each transcript in spleen. In the table, red shades indicate higher and green shades indicate lower mRNA levels as compared to the respective mRNA levels in spleen. The spleen mRNA levels are illustrated in the histogram on top of the table. Data in B represents means ± SEM. * indicated statistical significance p
    Cdnas, supplied by Evrogen, used in various techniques. Bioz Stars score: 92/100, based on 160 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GenScript cdnas
    PCB synthesis in mammalian cells. ( A ) The pathway of PCB synthesis in cyanobacteria. ( B ) Scheme for measurement of PCB fluorescence. The PhyB mutant PhyB-Y276H emits fluorescence from PCB when it binds to PCB. ( C ) Fluorescence images of PhyB-Y276H-mCherry-HRas C terminus (HRasCT) ( Upper ) and PCB fluorescence bound to PhyB-Y276H ( Lower ). (Scale bars, 25 μm.) ( D ) Quantification of PCB synthesis. PCB fluorescence bound to PhyB-Y276H was divided by mCherry fluorescence, followed by normalization to the average PCB-bound PhyB-Y276H/mCherry value of 2.5 μM PCB-treated cells. The box extends from the first to the third quartile, with the whiskers denoting 1.5 times the interquartile range. Red crosses are outliers. n = 24. ( E ) Structure of the pPHFF plasmid expressing MTS-PcyA, MTS-HO1, MTS-Fd, and <t>MTS-Fnr.</t> These <t>cDNAs</t> are connected by the cDNAs of a self-cleaving 2A peptide, P2A, which allows stoichiometric expression of multiple proteins flanking the 2A peptide. ( F ) Fluorescence images of PhyB-Y276H-mCherry-HRasCT ( Upper ) and PCB ( Lower ) are shown as in D . (Scale bars, 20 μm.) ( G ) PCB fluorescence in HeLa cells expressing PHFF was quantified as in D . n = 23.
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    Carcinoembryonic antigen-related cell adhesion molecule 1 <t>(CEACAM1)</t> level in human livers . Livers derived from anonymous obese (body mass index > 30 kg/m 2 ) 45- to 50-year-old male subjects and age-, sex-, and race-matched lean subjects. (A) CEACAM1 mRNA ( CC1 ) was analyzed by Northern blot analysis of total liver mRNA and sequentially probed with <t>cDNAs</t> for CEACAM1 ( CC1 ) followed by GAPDH for normalization. (B) Liver lysates from obese and lean subjects were analyzed by 4–12% SDS-PAGE followed by immunoblotting (Ib) with polyclonal antibody against CEACAM1 (CC1) and normalization against GAPDH. For simplicity, only two samples of each group are shown as representatives of three independent experiments. The graph on the right represents densitometry analysis of CEACAM1 bands relative to those of GAPDH in all tissues. Values shown as mean ± SEM with * P
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    Experimental design. Prostates from 12 mice from each of 5 strains of Mus musculus (C57BL/6, 129X1/Sv, BALB/c, FVB/N and DBA/2) were resected and individual lobes were dissected: DP, dorsal prostate; LP, lateral prostate; VP, ventral prostate; AP, anterior prostate. Each experimental sample represents a pool of equal amounts of RNA for each prostatic lobe from three animals. Four independent experimental samples were created per strain: 12 mice divided into 4 pools of 3 mice each for a total of 4 microarray experiments per strain. Amplified RNA from each experimental sample was hybridized against a reference pool onto custom mouse prostate <t>cDNA</t> <t>microarrays</t> using alternate dye-labeling to account for dye-specific effects.
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    Experimental design. Prostates from 12 mice from each of 5 strains of Mus musculus (C57BL/6, 129X1/Sv, BALB/c, FVB/N and DBA/2) were resected and individual lobes were dissected: DP, dorsal prostate; LP, lateral prostate; VP, ventral prostate; AP, anterior prostate. Each experimental sample represents a pool of equal amounts of RNA for each prostatic lobe from three animals. Four independent experimental samples were created per strain: 12 mice divided into 4 pools of 3 mice each for a total of 4 microarray experiments per strain. Amplified RNA from each experimental sample was hybridized against a reference pool onto custom mouse prostate <t>cDNA</t> <t>microarrays</t> using alternate dye-labeling to account for dye-specific effects.
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    Image Search Results


    SeT deletion in primary murine macrophages. (A) Representative graph of the murine Tnfα gene locus indicating the homology ( > 70%) with the human and chimpanzee genomes, mapping of the SeT lncRNA as well as the primer utilized for generating the SeT cDNA (RT) and the subsequent PCR products (1–6) with the SeT cDNA as template (blue: gene exons, yellow: untranslated regions, red: intergenic regions, arrows above genes: direction of gene transcription). (B) Diagrammatic representation of the targeting construct used for the SeT -/- mouse generation. (C) Genotyping of the mutated SeT mice. Detection by RT-PCR of the deletion of 1647 bp region in genomic extracts of primary macrophages isolated from the peritoneum (TEPMs) or the bone marrow (BMDMs) of CX3CR1-Cre SeT fl/fl mice and SeT -/- BMDMs. M: MW marker, WT: wild type, M1-M3/KO: different genomic DNA samples derived from mice bearing the deleted allele in homozygosity, HET: heterozygote sample (bearing one wild type and one deleted allele for SeT ), FX: floxed alleles. D) RT-PCR reactions for the detection of the relative mRNA levels for the lncRNA SeT and Hprt1 gene transcripts (mapping of PCR products is indicated in panel A).

    Journal: PLoS ONE

    Article Title: Long non-coding RNA SeT and miR-155 regulate the Tnfα gene allelic expression profile

    doi: 10.1371/journal.pone.0184788

    Figure Lengend Snippet: SeT deletion in primary murine macrophages. (A) Representative graph of the murine Tnfα gene locus indicating the homology ( > 70%) with the human and chimpanzee genomes, mapping of the SeT lncRNA as well as the primer utilized for generating the SeT cDNA (RT) and the subsequent PCR products (1–6) with the SeT cDNA as template (blue: gene exons, yellow: untranslated regions, red: intergenic regions, arrows above genes: direction of gene transcription). (B) Diagrammatic representation of the targeting construct used for the SeT -/- mouse generation. (C) Genotyping of the mutated SeT mice. Detection by RT-PCR of the deletion of 1647 bp region in genomic extracts of primary macrophages isolated from the peritoneum (TEPMs) or the bone marrow (BMDMs) of CX3CR1-Cre SeT fl/fl mice and SeT -/- BMDMs. M: MW marker, WT: wild type, M1-M3/KO: different genomic DNA samples derived from mice bearing the deleted allele in homozygosity, HET: heterozygote sample (bearing one wild type and one deleted allele for SeT ), FX: floxed alleles. D) RT-PCR reactions for the detection of the relative mRNA levels for the lncRNA SeT and Hprt1 gene transcripts (mapping of PCR products is indicated in panel A).

    Article Snippet: cDNA synthesis For quantitative Tnfα and SeT RNA expression analysis in WT, miR-155 -/- and SeT -/- murine macrophages, whole cell RNA was prepared using the TRI-REAGENT (SIGMA, T9424) following the manufacturer’s instructions.

    Techniques: Polymerase Chain Reaction, Construct, Mouse Assay, Reverse Transcription Polymerase Chain Reaction, Isolation, Marker, Derivative Assay

    Global analysis of fibroblast gene expression in response to IFN, gB, or HCMV infection. Intensity data from all of the cDNAs on the microarrays obtained at 8 and 24 h were log-transformed, and scatter plots were generated to assess differential gene expression between samples. Pair-wise similarity of gene-expression profiles was measured by the correlation coefficient; r ). The 2-h time points were omitted from this analysis because relatively few genes changed at this early time point.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Global modulation of cellular transcription by human cytomegalovirus is initiated by viral glycoprotein B

    doi: 10.1073/pnas.121177598

    Figure Lengend Snippet: Global analysis of fibroblast gene expression in response to IFN, gB, or HCMV infection. Intensity data from all of the cDNAs on the microarrays obtained at 8 and 24 h were log-transformed, and scatter plots were generated to assess differential gene expression between samples. Pair-wise similarity of gene-expression profiles was measured by the correlation coefficient; r ). The 2-h time points were omitted from this analysis because relatively few genes changed at this early time point.

    Article Snippet: The cDNAs printed on the microarrays were from the IMAGE consortium (Integrated Molecular Analysis of Genome and their Expression) and Incyte libraries.

    Techniques: Expressing, Infection, Transformation Assay, Generated

    Overexpression of caspases is not sufficient to accelerate islet cell apoptosis. 832/13 and primary rat islets were untreated (no virus) or treated with recombinant adenoviruses containing cDNAs corresponding to human Apaf-1, human caspase 3, human caspase 9 or the control gene, β-galactosidase (β-gal), as indicated. 72 h post-infection, 832/13 cells ( A ) and primary rat islets ( B ) were treated with DMSO (control) or thapsigargin (100 nM or 1 μM, respectively) for 18 h. Clarified lysates were examined by immunoblot analysis. Endogenous rat (r) and overexpressed human (h) proteins are labeled accordingly. Of note, Apaf-1 and caspase 9 antibodies only detect human (overexpressed) proteins. ( C , D ) 72 h post adenoviral infection, rat islets were treated with DMSO (control) or thapsigargin (1 μM) for up to 72 h. Islet cells were stained for TUNEL, caspase 3, and insulin and counterstained with DAPI. Cells were imaged using a high content imager and analyzed using Cellomics software. ( C ) Percentages of insulin+ TUNEL+ islet cells are shown. ( D ) Comparison of the percentages of caspase 3+ (overexpressing), TUNEL+ islet cells vs. caspase 3- (non-overexpressing), TUNEL+ islet cells are shown. ( C , D ) Data represent the mean +S.E.M. of 3 independent experiments. * p ≤ 0.05 as compared to DMSO treated cells.

    Journal: PLoS ONE

    Article Title: Delayed apoptosis allows islet β-cells to implement an autophagic mechanism to promote cell survival

    doi: 10.1371/journal.pone.0172567

    Figure Lengend Snippet: Overexpression of caspases is not sufficient to accelerate islet cell apoptosis. 832/13 and primary rat islets were untreated (no virus) or treated with recombinant adenoviruses containing cDNAs corresponding to human Apaf-1, human caspase 3, human caspase 9 or the control gene, β-galactosidase (β-gal), as indicated. 72 h post-infection, 832/13 cells ( A ) and primary rat islets ( B ) were treated with DMSO (control) or thapsigargin (100 nM or 1 μM, respectively) for 18 h. Clarified lysates were examined by immunoblot analysis. Endogenous rat (r) and overexpressed human (h) proteins are labeled accordingly. Of note, Apaf-1 and caspase 9 antibodies only detect human (overexpressed) proteins. ( C , D ) 72 h post adenoviral infection, rat islets were treated with DMSO (control) or thapsigargin (1 μM) for up to 72 h. Islet cells were stained for TUNEL, caspase 3, and insulin and counterstained with DAPI. Cells were imaged using a high content imager and analyzed using Cellomics software. ( C ) Percentages of insulin+ TUNEL+ islet cells are shown. ( D ) Comparison of the percentages of caspase 3+ (overexpressing), TUNEL+ islet cells vs. caspase 3- (non-overexpressing), TUNEL+ islet cells are shown. ( C , D ) Data represent the mean +S.E.M. of 3 independent experiments. * p ≤ 0.05 as compared to DMSO treated cells.

    Article Snippet: Plasmids containing cDNAs encoding caspase 3 (HsCD00043626) and caspase 9 (HsCD00043776) were from DNASU [ ]. cDNAs were recombined into pAd/CMV/V5-DEST (Thermo Life) using LR Clonase II plus (Thermo Life) per the manufacturer’s protocol [ ].

    Techniques: Over Expression, Recombinant, Infection, Labeling, Staining, TUNEL Assay, Software

    Attempts to Obtain Chicken Reprogrammed Cells with Various Delivery Systems Primary chicken embryonic fibroblasts (CEFs) were infected with the pLent polycistronic lentivirus. Colonies emerged (A) and expressed GFP (B), indicating that they were infected, although they failed to be amplified. More than 50 colonies were isolated in several independent experiments. Similarly, CEFs were infected with a cocktail of individual lentiviruses carrying mouse Oct4 , Sox2 , Klf4 , and c-Myc cDNAs. Compact colonies with AP-positive cells were obtained (C and D) but could not be established long term. In another attempt, CEFs were infected with pMX retroviruses carrying mouse Oct4 , Sox2 , Klf4 , and c-Myc . Morphological changes were rapidly observed (E), and colonies expanded once individually picked (F). The phenotypic changes were not stable, and cells reverted to a fibroblast phenotype (G) after four to six passages. Similarly, CEFs infected with Sendai viruses carrying human OCT4 , SOX2 , KLF4 , and c-MYC cDNAs exhibited morphological changes (H) but failed to be established and reverted to a fibroblast phenotype after a few passages. Scale bars, 50 μm.

    Journal: Stem Cell Reports

    Article Title: NANOG Is Required for the Long-Term Establishment of Avian Somatic Reprogrammed Cells

    doi: 10.1016/j.stemcr.2018.09.005

    Figure Lengend Snippet: Attempts to Obtain Chicken Reprogrammed Cells with Various Delivery Systems Primary chicken embryonic fibroblasts (CEFs) were infected with the pLent polycistronic lentivirus. Colonies emerged (A) and expressed GFP (B), indicating that they were infected, although they failed to be amplified. More than 50 colonies were isolated in several independent experiments. Similarly, CEFs were infected with a cocktail of individual lentiviruses carrying mouse Oct4 , Sox2 , Klf4 , and c-Myc cDNAs. Compact colonies with AP-positive cells were obtained (C and D) but could not be established long term. In another attempt, CEFs were infected with pMX retroviruses carrying mouse Oct4 , Sox2 , Klf4 , and c-Myc . Morphological changes were rapidly observed (E), and colonies expanded once individually picked (F). The phenotypic changes were not stable, and cells reverted to a fibroblast phenotype (G) after four to six passages. Similarly, CEFs infected with Sendai viruses carrying human OCT4 , SOX2 , KLF4 , and c-MYC cDNAs exhibited morphological changes (H) but failed to be established and reverted to a fibroblast phenotype after a few passages. Scale bars, 50 μm.

    Article Snippet: The cDNAs from chicken POUV ( POU5F3 ), SOX2 , SOX3 , KLF4 , c-MYC , NANOG , and LIN28 were cloned, sequenced, inserted into the pGAE lentivirus or pPB transposon backbones, and deposited to Addgene.

    Techniques: Infection, Amplification, Isolation

    Adapter-tRNA ligation efficiencies with a conventional method and YAMAT-seq. ( A ) Schematic representation of the adapter ligation reactions used in the conventional and YAMAT-seq methods. In the conventional method, tRNA was subjected to 3΄-adapter (3΄-AD) and 5΄-adapter (5΄-AD) ligations catalyzed by truncated Rnl2 and Rnl1, respectively, using the Illumina TruSeq Small RNA Sample Preparation Kit. In contrast, in the YAMAT-seq method, a Y-shaped adapter (Y-AD) is ligated to a tRNA by Rnl2. ( B ) Ligation products of synthetic human cyto tRNA AspGUC and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. The amounts of ligation products were determined based on standard curves, and ligation efficiencies were calculated as percentages of ligated tRNA versus input tRNA (set as 100%). Each data set represents the average of three independent experiments with bars showing the SD. ( C ) Ligation products of the indicated native cyto tRNAs in BT-474 total RNA and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. Each data set represents the average Ct values of three independent experiments with bars showing the SD. ( D ) Image of 8% native polyacrylamide gel electrophoresis (PAGE) of amplified cDNAs resulting from BT-474 total RNA sequencing by conventional and YAMAT-seq procedures. The total adapter lengths of the conventional and YAMAT-seq procedures are 118 and 140 bp, respectively. The YAMAT-seq-derived cDNAs in the designated Bands 1–3 regions were gel-purified and subjected to cloning; the identified sequences are shown in Supplementary Table S1 . The cDNAs in regions designated with gray lines are expected to contain tRNA fraction.

    Journal: Nucleic Acids Research

    Article Title: YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs

    doi: 10.1093/nar/gkx005

    Figure Lengend Snippet: Adapter-tRNA ligation efficiencies with a conventional method and YAMAT-seq. ( A ) Schematic representation of the adapter ligation reactions used in the conventional and YAMAT-seq methods. In the conventional method, tRNA was subjected to 3΄-adapter (3΄-AD) and 5΄-adapter (5΄-AD) ligations catalyzed by truncated Rnl2 and Rnl1, respectively, using the Illumina TruSeq Small RNA Sample Preparation Kit. In contrast, in the YAMAT-seq method, a Y-shaped adapter (Y-AD) is ligated to a tRNA by Rnl2. ( B ) Ligation products of synthetic human cyto tRNA AspGUC and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. The amounts of ligation products were determined based on standard curves, and ligation efficiencies were calculated as percentages of ligated tRNA versus input tRNA (set as 100%). Each data set represents the average of three independent experiments with bars showing the SD. ( C ) Ligation products of the indicated native cyto tRNAs in BT-474 total RNA and 5΄-AD or 3΄-AD were quantified by real-time qRT-PCR. Each data set represents the average Ct values of three independent experiments with bars showing the SD. ( D ) Image of 8% native polyacrylamide gel electrophoresis (PAGE) of amplified cDNAs resulting from BT-474 total RNA sequencing by conventional and YAMAT-seq procedures. The total adapter lengths of the conventional and YAMAT-seq procedures are 118 and 140 bp, respectively. The YAMAT-seq-derived cDNAs in the designated Bands 1–3 regions were gel-purified and subjected to cloning; the identified sequences are shown in Supplementary Table S1 . The cDNAs in regions designated with gray lines are expected to contain tRNA fraction.

    Article Snippet: Fourth, the resultant cDNAs are gel-purified and subjected to Illumina sequencing.

    Techniques: Ligation, Sample Prep, Quantitative RT-PCR, Polyacrylamide Gel Electrophoresis, Amplification, RNA Sequencing Assay, Derivative Assay, Purification, Clone Assay

    Amplification and sequencing of mature tRNAs using YAMAT-seq. ( A ) Image of 8% native PAGE of amplified cDNAs resulting from YAMAT-seq of total RNAs from MCF-7, SK-BR-3 and BT-20 cells. The result of one of the triplicate, Replicate 1 (R1), from each cell line is shown. The region designated with a gray line was subjected to gel-purification and Illumina sequencing. ( B ) Flow diagram of the read numbers filtered by the indicated sequence analyses. The result of R1 from each cell line is shown, whereas the results of R2 and R3 are shown in Supplementary Figure S1 . ( C ) Spearman's rank correlation analysis using tRNA reads of the technical triplicates (R1–R3) from each cell line. The results using the reads of all tRNAs (left), cyto tRNAs (middle) and mt tRNAs (right) are shown. The color bar indicates the strength of Spearman's correlation coefficient.

    Journal: Nucleic Acids Research

    Article Title: YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs

    doi: 10.1093/nar/gkx005

    Figure Lengend Snippet: Amplification and sequencing of mature tRNAs using YAMAT-seq. ( A ) Image of 8% native PAGE of amplified cDNAs resulting from YAMAT-seq of total RNAs from MCF-7, SK-BR-3 and BT-20 cells. The result of one of the triplicate, Replicate 1 (R1), from each cell line is shown. The region designated with a gray line was subjected to gel-purification and Illumina sequencing. ( B ) Flow diagram of the read numbers filtered by the indicated sequence analyses. The result of R1 from each cell line is shown, whereas the results of R2 and R3 are shown in Supplementary Figure S1 . ( C ) Spearman's rank correlation analysis using tRNA reads of the technical triplicates (R1–R3) from each cell line. The results using the reads of all tRNAs (left), cyto tRNAs (middle) and mt tRNAs (right) are shown. The color bar indicates the strength of Spearman's correlation coefficient.

    Article Snippet: Fourth, the resultant cDNAs are gel-purified and subjected to Illumina sequencing.

    Techniques: Amplification, Sequencing, Clear Native PAGE, Gel Purification, Flow Cytometry

    Experimental set up and overall expression profiles. (a) The time course of gene expression was determined during the response of two different fibroblast types; 2091 derived from foreskin and WI-38 derived from fetal lung. Each was treated with either the indicated GFs, epidermal growth factor (EGF), fibroblast growth factor (FGF), platelet derived growth factor (PDGF) or FBS (Serum), and three replicate time courses were run for each treatment. The layout of the samples in the other panels as well as in Figures 2-6 is as shown here. (b) Hierarchical cluster of 1,304 genes with a minimum expression change of twofold in at least 15 array experiments and with data present in at least 80% of all array samples. cDNAs with no known Unigene annotation or mapping to multiple Unigene clusters were removed. Black bars on the right indicate consistently induced genes. (c) Sub-cluster branches containing the consistently induced genes were selected and re-clustered. This set included 237 genes represented by 278 cDNA probes. (d) Consistently repressed genes were selected directly from expression data as described in Materials and methods and clustered. This set included 237 genes represented by 250 cDNA probes.

    Journal: Genome Biology

    Article Title: PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli

    doi: 10.1186/gb-2006-7-5-r42

    Figure Lengend Snippet: Experimental set up and overall expression profiles. (a) The time course of gene expression was determined during the response of two different fibroblast types; 2091 derived from foreskin and WI-38 derived from fetal lung. Each was treated with either the indicated GFs, epidermal growth factor (EGF), fibroblast growth factor (FGF), platelet derived growth factor (PDGF) or FBS (Serum), and three replicate time courses were run for each treatment. The layout of the samples in the other panels as well as in Figures 2-6 is as shown here. (b) Hierarchical cluster of 1,304 genes with a minimum expression change of twofold in at least 15 array experiments and with data present in at least 80% of all array samples. cDNAs with no known Unigene annotation or mapping to multiple Unigene clusters were removed. Black bars on the right indicate consistently induced genes. (c) Sub-cluster branches containing the consistently induced genes were selected and re-clustered. This set included 237 genes represented by 278 cDNA probes. (d) Consistently repressed genes were selected directly from expression data as described in Materials and methods and clustered. This set included 237 genes represented by 250 cDNA probes.

    Article Snippet: After removing cDNAs with no known Unigene annotation or those that matched multiple Unigene clusters, we were left with 1,304 cDNAs that were subjected to hierarchical clustering.

    Techniques: Expressing, Derivative Assay

    ( A ) C-type lectin receptors (CLR) mRNA expression in adult human tissues. Quantitative real-time PCR analysis was performed on pre-normalized cDNAs derived from poly(A)-selected DNase-treated RNAs purified from pools of healthy human tissues as described in methods; ( B ) CLR mRNA expression in adult mouse tissues. Real-time PCR was performed on pooled cDNAs derived from five adult six to eight week old C57BL/6 mice as described in methods. Biological replicates were quantified in triplicates and normalized to the respective GAPDH mRNA level. The results in the table are expressed relative to the respective expression level of each transcript in spleen. In the table, red shades indicate higher and green shades indicate lower mRNA levels as compared to the respective mRNA levels in spleen. The spleen mRNA levels are illustrated in the histogram on top of the table. Data in B represents means ± SEM. * indicated statistical significance p

    Journal: International Journal of Molecular Sciences

    Article Title: Quantitative Expression of C-Type Lectin Receptors in Humans and Mice

    doi: 10.3390/ijms130810113

    Figure Lengend Snippet: ( A ) C-type lectin receptors (CLR) mRNA expression in adult human tissues. Quantitative real-time PCR analysis was performed on pre-normalized cDNAs derived from poly(A)-selected DNase-treated RNAs purified from pools of healthy human tissues as described in methods; ( B ) CLR mRNA expression in adult mouse tissues. Real-time PCR was performed on pooled cDNAs derived from five adult six to eight week old C57BL/6 mice as described in methods. Biological replicates were quantified in triplicates and normalized to the respective GAPDH mRNA level. The results in the table are expressed relative to the respective expression level of each transcript in spleen. In the table, red shades indicate higher and green shades indicate lower mRNA levels as compared to the respective mRNA levels in spleen. The spleen mRNA levels are illustrated in the histogram on top of the table. Data in B represents means ± SEM. * indicated statistical significance p

    Article Snippet: Quantitative Real-Time RT-PCR Human solid organ prenormalized cDNAs derived from poly-(A)-selected DNase-treated RNAs purified from pools of healthy human tissues were obtained from Clontech, Mountain View, CA, USA.

    Techniques: Expressing, Real-time Polymerase Chain Reaction, Derivative Assay, Purification, Mouse Assay

    ( A ) CLRs mRNA expression in mouse kidney upon induction of IRI; ( B ) CLRs mRNA expression in mouse kidney upon induction of UUO; ( C ) CLRs mRNA expression in mouse kidney upon induction of lupus nephritis (LN). Real-time PCR was performed on cDNAs derived from murine kidney tissue from five to ten C57BL/6 mice that underwent ischemia reperfusion injury (IRI) (A), unilateral ureteral obstruction (UUO) (B) or progressive systemic autoimmunity with lupus nephritis in MRLlpr mice (C) as described in methods. Biological replicates were quantified and normalized to 18s rRNA level. The results in the table are expressed relative to the respective expression level of each transcript in sham operated kidney (A, B) or six week old MRLlpr mice (C). In the table, red shades indicate higher and green shades indicate lower mRNA levels as compared to the respective mRNA levels in spleen. Basal mRNA levels in control kidney are illustrated in the histogram below the table. Data in histograms represents means ± SEM. * In the tables indicates statistical significance p

    Journal: International Journal of Molecular Sciences

    Article Title: Quantitative Expression of C-Type Lectin Receptors in Humans and Mice

    doi: 10.3390/ijms130810113

    Figure Lengend Snippet: ( A ) CLRs mRNA expression in mouse kidney upon induction of IRI; ( B ) CLRs mRNA expression in mouse kidney upon induction of UUO; ( C ) CLRs mRNA expression in mouse kidney upon induction of lupus nephritis (LN). Real-time PCR was performed on cDNAs derived from murine kidney tissue from five to ten C57BL/6 mice that underwent ischemia reperfusion injury (IRI) (A), unilateral ureteral obstruction (UUO) (B) or progressive systemic autoimmunity with lupus nephritis in MRLlpr mice (C) as described in methods. Biological replicates were quantified and normalized to 18s rRNA level. The results in the table are expressed relative to the respective expression level of each transcript in sham operated kidney (A, B) or six week old MRLlpr mice (C). In the table, red shades indicate higher and green shades indicate lower mRNA levels as compared to the respective mRNA levels in spleen. Basal mRNA levels in control kidney are illustrated in the histogram below the table. Data in histograms represents means ± SEM. * In the tables indicates statistical significance p

    Article Snippet: Quantitative Real-Time RT-PCR Human solid organ prenormalized cDNAs derived from poly-(A)-selected DNase-treated RNAs purified from pools of healthy human tissues were obtained from Clontech, Mountain View, CA, USA.

    Techniques: Expressing, Real-time Polymerase Chain Reaction, Derivative Assay, Mouse Assay

    PCB synthesis in mammalian cells. ( A ) The pathway of PCB synthesis in cyanobacteria. ( B ) Scheme for measurement of PCB fluorescence. The PhyB mutant PhyB-Y276H emits fluorescence from PCB when it binds to PCB. ( C ) Fluorescence images of PhyB-Y276H-mCherry-HRas C terminus (HRasCT) ( Upper ) and PCB fluorescence bound to PhyB-Y276H ( Lower ). (Scale bars, 25 μm.) ( D ) Quantification of PCB synthesis. PCB fluorescence bound to PhyB-Y276H was divided by mCherry fluorescence, followed by normalization to the average PCB-bound PhyB-Y276H/mCherry value of 2.5 μM PCB-treated cells. The box extends from the first to the third quartile, with the whiskers denoting 1.5 times the interquartile range. Red crosses are outliers. n = 24. ( E ) Structure of the pPHFF plasmid expressing MTS-PcyA, MTS-HO1, MTS-Fd, and MTS-Fnr. These cDNAs are connected by the cDNAs of a self-cleaving 2A peptide, P2A, which allows stoichiometric expression of multiple proteins flanking the 2A peptide. ( F ) Fluorescence images of PhyB-Y276H-mCherry-HRasCT ( Upper ) and PCB ( Lower ) are shown as in D . (Scale bars, 20 μm.) ( G ) PCB fluorescence in HeLa cells expressing PHFF was quantified as in D . n = 23.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Efficient synthesis of phycocyanobilin in mammalian cells for optogenetic control of cell signaling

    doi: 10.1073/pnas.1707190114

    Figure Lengend Snippet: PCB synthesis in mammalian cells. ( A ) The pathway of PCB synthesis in cyanobacteria. ( B ) Scheme for measurement of PCB fluorescence. The PhyB mutant PhyB-Y276H emits fluorescence from PCB when it binds to PCB. ( C ) Fluorescence images of PhyB-Y276H-mCherry-HRas C terminus (HRasCT) ( Upper ) and PCB fluorescence bound to PhyB-Y276H ( Lower ). (Scale bars, 25 μm.) ( D ) Quantification of PCB synthesis. PCB fluorescence bound to PhyB-Y276H was divided by mCherry fluorescence, followed by normalization to the average PCB-bound PhyB-Y276H/mCherry value of 2.5 μM PCB-treated cells. The box extends from the first to the third quartile, with the whiskers denoting 1.5 times the interquartile range. Red crosses are outliers. n = 24. ( E ) Structure of the pPHFF plasmid expressing MTS-PcyA, MTS-HO1, MTS-Fd, and MTS-Fnr. These cDNAs are connected by the cDNAs of a self-cleaving 2A peptide, P2A, which allows stoichiometric expression of multiple proteins flanking the 2A peptide. ( F ) Fluorescence images of PhyB-Y276H-mCherry-HRasCT ( Upper ) and PCB ( Lower ) are shown as in D . (Scale bars, 20 μm.) ( G ) PCB fluorescence in HeLa cells expressing PHFF was quantified as in D . n = 23.

    Article Snippet: The cDNAs of Fd and Fnr of Synechocystis sp. PCC 6803 were synthesized with codon optimization for humans by GenScript.

    Techniques: Fluorescence, Mutagenesis, Plasmid Preparation, Expressing

    Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) level in human livers . Livers derived from anonymous obese (body mass index > 30 kg/m 2 ) 45- to 50-year-old male subjects and age-, sex-, and race-matched lean subjects. (A) CEACAM1 mRNA ( CC1 ) was analyzed by Northern blot analysis of total liver mRNA and sequentially probed with cDNAs for CEACAM1 ( CC1 ) followed by GAPDH for normalization. (B) Liver lysates from obese and lean subjects were analyzed by 4–12% SDS-PAGE followed by immunoblotting (Ib) with polyclonal antibody against CEACAM1 (CC1) and normalization against GAPDH. For simplicity, only two samples of each group are shown as representatives of three independent experiments. The graph on the right represents densitometry analysis of CEACAM1 bands relative to those of GAPDH in all tissues. Values shown as mean ± SEM with * P

    Journal: Frontiers in Endocrinology

    Article Title: Reduced Hepatic Carcinoembryonic Antigen-Related Cell Adhesion Molecule 1 Level in Obesity

    doi: 10.3389/fendo.2017.00054

    Figure Lengend Snippet: Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) level in human livers . Livers derived from anonymous obese (body mass index > 30 kg/m 2 ) 45- to 50-year-old male subjects and age-, sex-, and race-matched lean subjects. (A) CEACAM1 mRNA ( CC1 ) was analyzed by Northern blot analysis of total liver mRNA and sequentially probed with cDNAs for CEACAM1 ( CC1 ) followed by GAPDH for normalization. (B) Liver lysates from obese and lean subjects were analyzed by 4–12% SDS-PAGE followed by immunoblotting (Ib) with polyclonal antibody against CEACAM1 (CC1) and normalization against GAPDH. For simplicity, only two samples of each group are shown as representatives of three independent experiments. The graph on the right represents densitometry analysis of CEACAM1 bands relative to those of GAPDH in all tissues. Values shown as mean ± SEM with * P

    Article Snippet: Northern Blot Analysis of Rat Ceacam1 mRNA Level As previously described , Northern blot analysis was performed on total liver RNA extracted by TRIzol (Invitrogen), purified by MicroPoly (A) Pure Kit (Ambion), and sequentially probed with cDNAs for Ceacam1 followed by Gapdh for normalization, using the Random Primed DNA Labeling Kit (Roche).

    Techniques: Derivative Assay, Northern Blot, SDS Page

    Experimental design. Prostates from 12 mice from each of 5 strains of Mus musculus (C57BL/6, 129X1/Sv, BALB/c, FVB/N and DBA/2) were resected and individual lobes were dissected: DP, dorsal prostate; LP, lateral prostate; VP, ventral prostate; AP, anterior prostate. Each experimental sample represents a pool of equal amounts of RNA for each prostatic lobe from three animals. Four independent experimental samples were created per strain: 12 mice divided into 4 pools of 3 mice each for a total of 4 microarray experiments per strain. Amplified RNA from each experimental sample was hybridized against a reference pool onto custom mouse prostate cDNA microarrays using alternate dye-labeling to account for dye-specific effects.

    Journal: Genome Biology

    Article Title: Genetic background influences murine prostate gene expression: implications for cancer phenotypes

    doi: 10.1186/gb-2007-8-6-r117

    Figure Lengend Snippet: Experimental design. Prostates from 12 mice from each of 5 strains of Mus musculus (C57BL/6, 129X1/Sv, BALB/c, FVB/N and DBA/2) were resected and individual lobes were dissected: DP, dorsal prostate; LP, lateral prostate; VP, ventral prostate; AP, anterior prostate. Each experimental sample represents a pool of equal amounts of RNA for each prostatic lobe from three animals. Four independent experimental samples were created per strain: 12 mice divided into 4 pools of 3 mice each for a total of 4 microarray experiments per strain. Amplified RNA from each experimental sample was hybridized against a reference pool onto custom mouse prostate cDNA microarrays using alternate dye-labeling to account for dye-specific effects.

    Article Snippet: The 20 microarrays used for the experiment were all from the same printing batch. cDNA probes were made from 2 μg of amplified RNA in a reaction volume of 30 μl containing 170 ng random hexamer primers, 0.2 mM 5-(3-aminoallyl)-2-deoxyuridine-5-triphosphate (amino acid-dUTP; Sigma-Aldrich, St. Louis, MO), 0.3 mM dTTP, 0.5 mM each dATP, dCTP, and dGTP, and 380 units of Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) incubated at 42°C for 120 minutes.

    Techniques: Mouse Assay, Microarray, Amplification, Labeling