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  • 88
    TaKaRa primer1
    Primer1, supplied by TaKaRa, used in various techniques. Bioz Stars score: 88/100, based on 45 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    GE Healthcare primer1 ggtgcggggaa
    Primer1 Ggtgcggggaa, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Illumina Inc truseq adapter primer1
    Truseq Adapter Primer1, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    PrimerDesign Inc programme primer1 primer design
    Programme Primer1 Primer Design, supplied by PrimerDesign Inc, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    TaKaRa nested pcr primer1
    Nested Pcr Primer1, supplied by TaKaRa, used in various techniques. Bioz Stars score: 85/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc primer 1
    Primer 1, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    HY Labs primer 1
    Primer 1, supplied by HY Labs, used in various techniques. Bioz Stars score: 91/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Beijing SBS Genetech primer 1
    Primer 1, supplied by Beijing SBS Genetech, used in various techniques. Bioz Stars score: 90/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    TaKaRa cds primer 1
    Cds Primer 1, supplied by TaKaRa, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    TaKaRa adaptor primer 1
    Adaptor Primer 1, supplied by TaKaRa, used in various techniques. Bioz Stars score: 85/100, based on 46 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    TaKaRa nested primer 1
    Nested Primer 1, supplied by TaKaRa, used in various techniques. Bioz Stars score: 88/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Millipore primer 1 0
    Primer 1 0, supplied by Millipore, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc multiplex primer 1 0
    Multiplex Primer 1 0, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc pe primer 1 0
    Pe Primer 1 0, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 83 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Roche primer 1
    Mitochondrial localization of the ncmtRNA. ( a ) The mitochondrial fraction from HeLa cells was treated with RNase A, previously to RNA extraction. Amplification of the mitochondrial RNA with <t>primer</t> 1 in combination with primer 4 (lanes 1 and 2) or primer 5 (lanes 3 and 4) yielded the expected amplicons of 700 and 800 bp, respectively. No amplification was obtained with primers 1 and 6 (lanes 5 and 6) or when the reaction was carried out without reverse transcriptase (RT−, lanes 2, 4 and 6). ( b ) Total RNA extracted from two different preparations of HeLa mitochondria (lanes 1and 2, and 3 and 4) treated without (lanes 1 and 3) or with RNase A (lanes 2 and 4) was used to amplify the 215 bp fragment of the ncmtRNA, and the indicated amplicons of COX I mRNA, 18S rRNA and β-actin mRNA. Note that RNase A treatment abolished contamination with cytoplasmic transcripts. ( c ) Co-localization of the ncmtRNA with the mitochondrial markers cytochrome c and endonuclease G. HeLa cells were subjected to FISH to detect the ncmtRNA and immunocytochemistry to detect cytochrome c or endonuclease G (see Methods section) and analyzed by confocal microscopy.
    Primer 1, supplied by Roche, used in various techniques. Bioz Stars score: 91/100, based on 95 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Roche ⋅primer 1
    Mitochondrial localization of the ncmtRNA. ( a ) The mitochondrial fraction from HeLa cells was treated with RNase A, previously to RNA extraction. Amplification of the mitochondrial RNA with <t>primer</t> 1 in combination with primer 4 (lanes 1 and 2) or primer 5 (lanes 3 and 4) yielded the expected amplicons of 700 and 800 bp, respectively. No amplification was obtained with primers 1 and 6 (lanes 5 and 6) or when the reaction was carried out without reverse transcriptase (RT−, lanes 2, 4 and 6). ( b ) Total RNA extracted from two different preparations of HeLa mitochondria (lanes 1and 2, and 3 and 4) treated without (lanes 1 and 3) or with RNase A (lanes 2 and 4) was used to amplify the 215 bp fragment of the ncmtRNA, and the indicated amplicons of COX I mRNA, 18S rRNA and β-actin mRNA. Note that RNase A treatment abolished contamination with cytoplasmic transcripts. ( c ) Co-localization of the ncmtRNA with the mitochondrial markers cytochrome c and endonuclease G. HeLa cells were subjected to FISH to detect the ncmtRNA and immunocytochemistry to detect cytochrome c or endonuclease G (see Methods section) and analyzed by confocal microscopy.
    ⋅Primer 1, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    GenScript primer 1
    Mitochondrial localization of the ncmtRNA. ( a ) The mitochondrial fraction from HeLa cells was treated with RNase A, previously to RNA extraction. Amplification of the mitochondrial RNA with <t>primer</t> 1 in combination with primer 4 (lanes 1 and 2) or primer 5 (lanes 3 and 4) yielded the expected amplicons of 700 and 800 bp, respectively. No amplification was obtained with primers 1 and 6 (lanes 5 and 6) or when the reaction was carried out without reverse transcriptase (RT−, lanes 2, 4 and 6). ( b ) Total RNA extracted from two different preparations of HeLa mitochondria (lanes 1and 2, and 3 and 4) treated without (lanes 1 and 3) or with RNase A (lanes 2 and 4) was used to amplify the 215 bp fragment of the ncmtRNA, and the indicated amplicons of COX I mRNA, 18S rRNA and β-actin mRNA. Note that RNase A treatment abolished contamination with cytoplasmic transcripts. ( c ) Co-localization of the ncmtRNA with the mitochondrial markers cytochrome c and endonuclease G. HeLa cells were subjected to FISH to detect the ncmtRNA and immunocytochemistry to detect cytochrome c or endonuclease G (see Methods section) and analyzed by confocal microscopy.
    Primer 1, supplied by GenScript, used in various techniques. Bioz Stars score: 90/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher primer 1
    Density plots of oligonucleotide probes sets hybridized with RNA amplified with indicated T7 primers (listed in fig 2 ). Horizontal axis is the log intensity scale. A and B, platforms that show T7 primer 3′spacer sequence bias, C and D, platforms that show little or no T7 primer 3′spacer sequence bias. Density analyses were performed on oligonucleotides containing 6 mer sequences (A and C), and on 9-mer sequences (B and D) based on the 3′spacer sequences from <t>primer</t> 1 and 2 (blue) or primer 3 and 4 (red). Arrows indicate the right-shifted density lines for the probes having the 3′spacer sequence present in the primer that was used in the study (indicated at the top of the graphs). Control lines are plotted in black, grey or pink lines. The black line represents density data for all probes lacking T7 motifs; the pink lines are individual random motifs for 6-mer or 9-mer sequences (n = 50), and the grey lines represents data from individual random probes (n = equal to the size of the subset of probes containing the T7 motif used in the study).
    Primer 1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 265 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Sigma-Genosys primer 1
    Density plots of oligonucleotide probes sets hybridized with RNA amplified with indicated T7 primers (listed in fig 2 ). Horizontal axis is the log intensity scale. A and B, platforms that show T7 primer 3′spacer sequence bias, C and D, platforms that show little or no T7 primer 3′spacer sequence bias. Density analyses were performed on oligonucleotides containing 6 mer sequences (A and C), and on 9-mer sequences (B and D) based on the 3′spacer sequences from <t>primer</t> 1 and 2 (blue) or primer 3 and 4 (red). Arrows indicate the right-shifted density lines for the probes having the 3′spacer sequence present in the primer that was used in the study (indicated at the top of the graphs). Control lines are plotted in black, grey or pink lines. The black line represents density data for all probes lacking T7 motifs; the pink lines are individual random motifs for 6-mer or 9-mer sequences (n = 50), and the grey lines represents data from individual random probes (n = equal to the size of the subset of probes containing the T7 motif used in the study).
    Primer 1, supplied by Sigma-Genosys, used in various techniques. Bioz Stars score: 91/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/primer 1/product/Sigma-Genosys
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    Image Search Results


    Mitochondrial localization of the ncmtRNA. ( a ) The mitochondrial fraction from HeLa cells was treated with RNase A, previously to RNA extraction. Amplification of the mitochondrial RNA with primer 1 in combination with primer 4 (lanes 1 and 2) or primer 5 (lanes 3 and 4) yielded the expected amplicons of 700 and 800 bp, respectively. No amplification was obtained with primers 1 and 6 (lanes 5 and 6) or when the reaction was carried out without reverse transcriptase (RT−, lanes 2, 4 and 6). ( b ) Total RNA extracted from two different preparations of HeLa mitochondria (lanes 1and 2, and 3 and 4) treated without (lanes 1 and 3) or with RNase A (lanes 2 and 4) was used to amplify the 215 bp fragment of the ncmtRNA, and the indicated amplicons of COX I mRNA, 18S rRNA and β-actin mRNA. Note that RNase A treatment abolished contamination with cytoplasmic transcripts. ( c ) Co-localization of the ncmtRNA with the mitochondrial markers cytochrome c and endonuclease G. HeLa cells were subjected to FISH to detect the ncmtRNA and immunocytochemistry to detect cytochrome c or endonuclease G (see Methods section) and analyzed by confocal microscopy.

    Journal: Nucleic Acids Research

    Article Title: Expression of a novel non-coding mitochondrial RNA in human proliferating cells

    doi: 10.1093/nar/gkm863

    Figure Lengend Snippet: Mitochondrial localization of the ncmtRNA. ( a ) The mitochondrial fraction from HeLa cells was treated with RNase A, previously to RNA extraction. Amplification of the mitochondrial RNA with primer 1 in combination with primer 4 (lanes 1 and 2) or primer 5 (lanes 3 and 4) yielded the expected amplicons of 700 and 800 bp, respectively. No amplification was obtained with primers 1 and 6 (lanes 5 and 6) or when the reaction was carried out without reverse transcriptase (RT−, lanes 2, 4 and 6). ( b ) Total RNA extracted from two different preparations of HeLa mitochondria (lanes 1and 2, and 3 and 4) treated without (lanes 1 and 3) or with RNase A (lanes 2 and 4) was used to amplify the 215 bp fragment of the ncmtRNA, and the indicated amplicons of COX I mRNA, 18S rRNA and β-actin mRNA. Note that RNase A treatment abolished contamination with cytoplasmic transcripts. ( c ) Co-localization of the ncmtRNA with the mitochondrial markers cytochrome c and endonuclease G. HeLa cells were subjected to FISH to detect the ncmtRNA and immunocytochemistry to detect cytochrome c or endonuclease G (see Methods section) and analyzed by confocal microscopy.

    Article Snippet: First, an amplicon was obtained by RT-PCR using primers 1 and 2 and this fragment was used as a template in an asymmetric PCR reaction that contained only primer 1 and digoxigenin-11-dUTP (Roche Non-Radioactive ISH).

    Techniques: RNA Extraction, Amplification, Fluorescence In Situ Hybridization, Immunocytochemistry, Confocal Microscopy

    Synthesis of the ncmtRNA requires mitochondrial transcription. ( a ) Total RNA was extracted from HeLa cells incubated without (odd lanes) or with (even lanes) 1 μg/ml of ethidium bromide for 28 days. The RNA was amplified by RT-PCR using specific primers for 18S rRNA (lanes 1 and 2) (see Methods section), primers 9 and 11 (lanes 3 and 4) and primers 1 and 2 for the ncmtRNA (lanes 5 and 6). ( b ) Theoretical structure of an anomalous mtDNA containing an insert of 815 bp between the tRNA val and the 16S mtrRNA genes. ( c ) mtDNA from the indicated cell lines was amplified between primer 16 positioned close to the 3′ end of the 12S gene and primer 1 positioned on the 16S mtrRNA gene as shown in (b). All samples yielded a single amplicon of 128 nt. (a) M, 100 bp ladder. (c) 50 bp ladder.

    Journal: Nucleic Acids Research

    Article Title: Expression of a novel non-coding mitochondrial RNA in human proliferating cells

    doi: 10.1093/nar/gkm863

    Figure Lengend Snippet: Synthesis of the ncmtRNA requires mitochondrial transcription. ( a ) Total RNA was extracted from HeLa cells incubated without (odd lanes) or with (even lanes) 1 μg/ml of ethidium bromide for 28 days. The RNA was amplified by RT-PCR using specific primers for 18S rRNA (lanes 1 and 2) (see Methods section), primers 9 and 11 (lanes 3 and 4) and primers 1 and 2 for the ncmtRNA (lanes 5 and 6). ( b ) Theoretical structure of an anomalous mtDNA containing an insert of 815 bp between the tRNA val and the 16S mtrRNA genes. ( c ) mtDNA from the indicated cell lines was amplified between primer 16 positioned close to the 3′ end of the 12S gene and primer 1 positioned on the 16S mtrRNA gene as shown in (b). All samples yielded a single amplicon of 128 nt. (a) M, 100 bp ladder. (c) 50 bp ladder.

    Article Snippet: First, an amplicon was obtained by RT-PCR using primers 1 and 2 and this fragment was used as a template in an asymmetric PCR reaction that contained only primer 1 and digoxigenin-11-dUTP (Roche Non-Radioactive ISH).

    Techniques: Incubation, Amplification, Reverse Transcription Polymerase Chain Reaction

    The human ncmtRNA. ( a ) Theoretical structure of the human ncmtRNA. The 5′ end of the sense 16S mtrRNA (red line) is linked to a fragment of the antisense 16S mtrRNA or IR (blue line) forming a double-stranded structure and a loop of unknown length. The position of the reverse primers (under the lines) and the forward primers (over the lines) are indicated (see Materials and Methods section). ( b ) Digestion of the loop and the single-stranded region of the ncmtRNA by RNase A is also illustrated. ( c ) Amplification of the cDNA obtained from three tumor cell lines using primers 1 and 2. An amplicon of ∼210 bp was obtained only when the reaction was carried out with reverse transcriptase (c, odd lanes). ( d ) Amplification of the cDNA of HeLa cells by PCR using primers 1 in combination with primers 3 (lanes 1 and 2), 4 (lanes 3 and 4), 5 (lanes 5 and 6) and 6 (lanes 7 and 8), respectively. Amplicons of ∼500, 700 and 800 bp were obtained. No amplification products were generated with primer 1 and 6 (lanes 7 and 8) or without reverse transcriptase (d, even lanes). M, 100 bp ladder. ( e ) RNA from HeLa cells in 2× SSC was incubated without (odd lanes) or with 50 μg/ml of RNase A for 15 min at 25°C (even lanes). The RNA was recovered and amplified by RT-PCR using primers 1 and 5 (lanes 1 and 2), primers 10 and 11 (lanes 3 and 4) or with primers 7 and 5 (lanes 5 and 6). Amplicons of 800 and 350 bp were obtained with primer 1 and 5, and 10 and 11, respectively, only with untreated RNA (lanes 1 and 3, respectively). Amplification of the fragment of 750 bp obtained with primers 7 and 5 was not affected by the nuclease treatment (lanes 5 and 6). f) Amplification of the 12S mtrRNA (lanes 1 and 2), 18S rRNA (lanes 3 and 4) and GAPDH mRNA (lanes 5 and 6) after digestion with RNase A (mock experiment, odd lanes). ( g ) About 1 μg of RNA from the indicated cell lines was digested with RNase A and the digestion products were resolved by electrophoresis on a 1.5% agarose gel. After blotting, the membrane was probed with a 32 P-labeled PCR fragment targeted to the double-stranded region of the ncmtRNA (see Materials Methods section). A single hybridization band corresponding to a transcript of ∼800 nt was detected.

    Journal: Nucleic Acids Research

    Article Title: Expression of a novel non-coding mitochondrial RNA in human proliferating cells

    doi: 10.1093/nar/gkm863

    Figure Lengend Snippet: The human ncmtRNA. ( a ) Theoretical structure of the human ncmtRNA. The 5′ end of the sense 16S mtrRNA (red line) is linked to a fragment of the antisense 16S mtrRNA or IR (blue line) forming a double-stranded structure and a loop of unknown length. The position of the reverse primers (under the lines) and the forward primers (over the lines) are indicated (see Materials and Methods section). ( b ) Digestion of the loop and the single-stranded region of the ncmtRNA by RNase A is also illustrated. ( c ) Amplification of the cDNA obtained from three tumor cell lines using primers 1 and 2. An amplicon of ∼210 bp was obtained only when the reaction was carried out with reverse transcriptase (c, odd lanes). ( d ) Amplification of the cDNA of HeLa cells by PCR using primers 1 in combination with primers 3 (lanes 1 and 2), 4 (lanes 3 and 4), 5 (lanes 5 and 6) and 6 (lanes 7 and 8), respectively. Amplicons of ∼500, 700 and 800 bp were obtained. No amplification products were generated with primer 1 and 6 (lanes 7 and 8) or without reverse transcriptase (d, even lanes). M, 100 bp ladder. ( e ) RNA from HeLa cells in 2× SSC was incubated without (odd lanes) or with 50 μg/ml of RNase A for 15 min at 25°C (even lanes). The RNA was recovered and amplified by RT-PCR using primers 1 and 5 (lanes 1 and 2), primers 10 and 11 (lanes 3 and 4) or with primers 7 and 5 (lanes 5 and 6). Amplicons of 800 and 350 bp were obtained with primer 1 and 5, and 10 and 11, respectively, only with untreated RNA (lanes 1 and 3, respectively). Amplification of the fragment of 750 bp obtained with primers 7 and 5 was not affected by the nuclease treatment (lanes 5 and 6). f) Amplification of the 12S mtrRNA (lanes 1 and 2), 18S rRNA (lanes 3 and 4) and GAPDH mRNA (lanes 5 and 6) after digestion with RNase A (mock experiment, odd lanes). ( g ) About 1 μg of RNA from the indicated cell lines was digested with RNase A and the digestion products were resolved by electrophoresis on a 1.5% agarose gel. After blotting, the membrane was probed with a 32 P-labeled PCR fragment targeted to the double-stranded region of the ncmtRNA (see Materials Methods section). A single hybridization band corresponding to a transcript of ∼800 nt was detected.

    Article Snippet: First, an amplicon was obtained by RT-PCR using primers 1 and 2 and this fragment was used as a template in an asymmetric PCR reaction that contained only primer 1 and digoxigenin-11-dUTP (Roche Non-Radioactive ISH).

    Techniques: Amplification, Polymerase Chain Reaction, Generated, Incubation, Reverse Transcription Polymerase Chain Reaction, Electrophoresis, Agarose Gel Electrophoresis, Labeling, Hybridization

    Density plots of oligonucleotide probes sets hybridized with RNA amplified with indicated T7 primers (listed in fig 2 ). Horizontal axis is the log intensity scale. A and B, platforms that show T7 primer 3′spacer sequence bias, C and D, platforms that show little or no T7 primer 3′spacer sequence bias. Density analyses were performed on oligonucleotides containing 6 mer sequences (A and C), and on 9-mer sequences (B and D) based on the 3′spacer sequences from primer 1 and 2 (blue) or primer 3 and 4 (red). Arrows indicate the right-shifted density lines for the probes having the 3′spacer sequence present in the primer that was used in the study (indicated at the top of the graphs). Control lines are plotted in black, grey or pink lines. The black line represents density data for all probes lacking T7 motifs; the pink lines are individual random motifs for 6-mer or 9-mer sequences (n = 50), and the grey lines represents data from individual random probes (n = equal to the size of the subset of probes containing the T7 motif used in the study).

    Journal: PLoS ONE

    Article Title: The T7-Primer Is a Source of Experimental Bias and Introduces Variability between Microarray Platforms

    doi: 10.1371/journal.pone.0001980

    Figure Lengend Snippet: Density plots of oligonucleotide probes sets hybridized with RNA amplified with indicated T7 primers (listed in fig 2 ). Horizontal axis is the log intensity scale. A and B, platforms that show T7 primer 3′spacer sequence bias, C and D, platforms that show little or no T7 primer 3′spacer sequence bias. Density analyses were performed on oligonucleotides containing 6 mer sequences (A and C), and on 9-mer sequences (B and D) based on the 3′spacer sequences from primer 1 and 2 (blue) or primer 3 and 4 (red). Arrows indicate the right-shifted density lines for the probes having the 3′spacer sequence present in the primer that was used in the study (indicated at the top of the graphs). Control lines are plotted in black, grey or pink lines. The black line represents density data for all probes lacking T7 motifs; the pink lines are individual random motifs for 6-mer or 9-mer sequences (n = 50), and the grey lines represents data from individual random probes (n = equal to the size of the subset of probes containing the T7 motif used in the study).

    Article Snippet: The “Affymetrix” study uses primer 1, and again we observe a shift of 3.6 for the corresponding motif containing probes ( ).

    Techniques: Amplification, Sequencing