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  • 99
    Thermo Fisher high capacity complementary dna reverse transcription kit
    High Capacity Complementary Dna Reverse Transcription Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2349 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad iscript cdna synthesis kit
    Iscript Cdna Synthesis Kit, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 95548 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher first strand cdna
    First Strand Cdna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 86469 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher revertaid first strand cdna synthesis kit
    Revertaid First Strand Cdna Synthesis Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 40122 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher cdna synthesis
    Cdna Synthesis, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 106131 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher cdna
    Cdna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 160058 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc cdna libraries
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Cdna Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 30682 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher high capacity rna to cdna kit
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    High Capacity Rna To Cdna Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 18369 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher superscript vilo cdna synthesis kit
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Superscript Vilo Cdna Synthesis Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 17594 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher cdna synthesis kit
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Cdna Synthesis Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 10193 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher maxima first strand cdna synthesis kit
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Maxima First Strand Cdna Synthesis Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 9764 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher revertaid h minus first strand cdna synthesis kit
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Revertaid H Minus First Strand Cdna Synthesis Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 9555 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher rapid amplification
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Rapid Amplification, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 12314 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher cdna ends
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Cdna Ends, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 9717 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Quanta Biosciences qscript cdna supermix
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Qscript Cdna Supermix, supplied by Quanta Biosciences, used in various techniques. Bioz Stars score: 94/100, based on 7210 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    TaKaRa smart race cdna amplification kit
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Smart Race Cdna Amplification Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 9386 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa primescript 1st strand cdna synthesis kit
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Primescript 1st Strand Cdna Synthesis Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 7752 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher cdna libraries
    Viral <t>RNA</t> fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate <t>cDNA</t> synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.
    Cdna Libraries, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5482 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Bio-Rad cdnas
    Domains show conservation and expression tendencies. (A) Relationship between gene frequency and AT content in microarrays hybridized with <t>cDNAs</t> obtained from total <t>RNA.</t> (B) Relationship between average FU and AT content in microarrays hybridized with cDNAs obtained from total RNA. A window of 11 genes (average value on the middle one) was applied for FU values. Only coding regions were considered in the AT calculations. (C) Relationship between FU value and AT content in microarrays hybridized with cDNA obtained from total DNA, the median of about 32 microarray spot values was calculated and the mean of medians from two replicates considered. (D) Relationship between the gene lack index and FU. Genes were considered equivalent to R6 counterparts when their polypeptide products shared ≥80% identity over ≥80% of the sequence length in other S. pneumoniae strains with complete genome sequence: 70585, ATCC 700669, CGSP14, D39, G54, Hungary19A-6, JJA, P1031, Taiwan19F-14, TCH8431/19A and TIGR4. An 11-gene window (roughly equivalent to 10 Kb) was applied. Misleading continuum of sharp peaks or poorly defined peaks were obtained when narrower or wider windows were applied, respectively.
    Cdnas, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 94/100, based on 8564 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Viral RNA fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate cDNA synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.

    Journal: Nucleic Acids Research

    Article Title: Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs

    doi: 10.1093/nar/gku118

    Figure Lengend Snippet: Viral RNA fragments produced by RNase L and RNase A. HCV and PV RNAs were incubated with RNase L and RNase A to produce RNA fragments for 2′, 3′-cyclic phosphate cDNA synthesis and sequencing. Agarose gel electrophoresis and ethidium bromide staining revealed the size of viral RNA fragments. ( A ) Diagram of HCV and PV RNAs. HCV RNA is 9648 bases long. PV RNA is 7500 bases long. ( B ) Viral RNAs incubated with RNase L. HCV and PV RNAs were incubated with RNase L for 20 min in the absence of 2-5A (no 2-5A), or with RNase L and 2-5A for 0, 2.5, 5, 10 and 20 min. ( C ) Viral RNAs incubated with RNase A. HCV and PV RNAs were incubated for 20 min in the absence of RNase A (−), and the presence of RNase A for 0, 2.5, 5, 10 and 20 min.

    Article Snippet: We exploited the 2′, 3′-cyclic phosphates at RNA cleavage sites to make cDNA libraries suitable for Illumina sequencing ( Supplementary Figure S1 ).

    Techniques: Produced, Incubation, Sequencing, Agarose Gel Electrophoresis, Staining

    Endoribonuclease cleavage sites in PV RNA isolated from HeLa cells. RNAs from PV-infected HeLa cells ( Figure 3 B) were used for 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing. ( A ) Location and frequency of cleavage sites in PV RNA from W12 HeLa cells. X-axis: Nucleotide position in PV RNA. Y-axis: Number of distinct UMI-tagged linkers detected at each cleavage site. ( B ) Dinucleotide specificity of cleavage sites in PV RNA from W12 HeLa cells. X-axis: Dinucleotide at the 3′-end of PV RNA fragments (adjacent to 8 base UMI sequence in RNA linkers as illustrated in Supplementary Figure S1 ). Y-axis: Percent of PV cDNA reads. ( C ) Location and frequency of cleavage sites in PV RNA from M25 HeLa cells. X-axis: Nucleotide position in PV RNA. Y-axis: Number of distinct UMI-tagged linkers detected at each cleavage site. ( D ) Dinucleotide specificity of cleavage sites in PV RNA from M25 HeLa cells. X-axis: Dinucleotide at the 3′-end of PV RNA fragments. Y-axis: Percent of PV cDNA reads.

    Journal: Nucleic Acids Research

    Article Title: Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs

    doi: 10.1093/nar/gku118

    Figure Lengend Snippet: Endoribonuclease cleavage sites in PV RNA isolated from HeLa cells. RNAs from PV-infected HeLa cells ( Figure 3 B) were used for 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing. ( A ) Location and frequency of cleavage sites in PV RNA from W12 HeLa cells. X-axis: Nucleotide position in PV RNA. Y-axis: Number of distinct UMI-tagged linkers detected at each cleavage site. ( B ) Dinucleotide specificity of cleavage sites in PV RNA from W12 HeLa cells. X-axis: Dinucleotide at the 3′-end of PV RNA fragments (adjacent to 8 base UMI sequence in RNA linkers as illustrated in Supplementary Figure S1 ). Y-axis: Percent of PV cDNA reads. ( C ) Location and frequency of cleavage sites in PV RNA from M25 HeLa cells. X-axis: Nucleotide position in PV RNA. Y-axis: Number of distinct UMI-tagged linkers detected at each cleavage site. ( D ) Dinucleotide specificity of cleavage sites in PV RNA from M25 HeLa cells. X-axis: Dinucleotide at the 3′-end of PV RNA fragments. Y-axis: Percent of PV cDNA reads.

    Article Snippet: We exploited the 2′, 3′-cyclic phosphates at RNA cleavage sites to make cDNA libraries suitable for Illumina sequencing ( Supplementary Figure S1 ).

    Techniques: Isolation, Infection, Sequencing

    Endoribonuclease cleavage sites in rRNAs from M25 HeLa cells. RNAs from mock-infected and PV-infected M25 HeLa cells ( Figure 3 B) were used for 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing. The location and frequency of cleavage sites in 28S rRNA ( A ), 18S rRNA ( B ), 5.8S rRNA ( C ) and 5S rRNA ( D ) are shown for mock-infected and PV-infected RNA samples isolated at 8 hpa. X-axis: Nucleotide position of each RNA. Y-axis: Percentage of total UMIs at each cleavage site. Dinucleotides at the 3′-end of abundant RNA fragments are annotated at the corresponding positions in the graphs. The locations of GC-rich expansion segments are highlighted by light blue rectangles.

    Journal: Nucleic Acids Research

    Article Title: Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs

    doi: 10.1093/nar/gku118

    Figure Lengend Snippet: Endoribonuclease cleavage sites in rRNAs from M25 HeLa cells. RNAs from mock-infected and PV-infected M25 HeLa cells ( Figure 3 B) were used for 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing. The location and frequency of cleavage sites in 28S rRNA ( A ), 18S rRNA ( B ), 5.8S rRNA ( C ) and 5S rRNA ( D ) are shown for mock-infected and PV-infected RNA samples isolated at 8 hpa. X-axis: Nucleotide position of each RNA. Y-axis: Percentage of total UMIs at each cleavage site. Dinucleotides at the 3′-end of abundant RNA fragments are annotated at the corresponding positions in the graphs. The locations of GC-rich expansion segments are highlighted by light blue rectangles.

    Article Snippet: We exploited the 2′, 3′-cyclic phosphates at RNA cleavage sites to make cDNA libraries suitable for Illumina sequencing ( Supplementary Figure S1 ).

    Techniques: Infection, Sequencing, Isolation

    Frequency, location and dinucleotide specificity of cleavage sites in viral RNAs. 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing was used to analyze the viral RNA fragments shown in Figure 1 . ( A ) Frequency, location and dinucleotide specificity of endoribonuclease cleavage sites in HCV RNA (from 20 min samples). ( B ) Frequency, location and dinucleotide specificity of cleavage sites in PV RNA (from 20 min samples).

    Journal: Nucleic Acids Research

    Article Title: Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs

    doi: 10.1093/nar/gku118

    Figure Lengend Snippet: Frequency, location and dinucleotide specificity of cleavage sites in viral RNAs. 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing was used to analyze the viral RNA fragments shown in Figure 1 . ( A ) Frequency, location and dinucleotide specificity of endoribonuclease cleavage sites in HCV RNA (from 20 min samples). ( B ) Frequency, location and dinucleotide specificity of cleavage sites in PV RNA (from 20 min samples).

    Article Snippet: We exploited the 2′, 3′-cyclic phosphates at RNA cleavage sites to make cDNA libraries suitable for Illumina sequencing ( Supplementary Figure S1 ).

    Techniques: Sequencing

    Endoribonuclease cleavage sites in rRNAs from W12 HeLa cells. RNAs from mock-infected and PV-infected W12 HeLa cells ( Figure 3 B) were used for 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing. The location and frequency of cleavage sites in 28S rRNA ( A ), 18S rRNA ( B ), 5.8S rRNA ( C ) and 5S rRNA ( D ) are shown for mock-infected and PV-infected RNA samples isolated at 8 hpa. X-axis: Nucleotide position of each RNA. Y-axis: Percentage of total UMIs at each cleavage site. Dinucleotides at the 3′-end of abundant RNA fragments are annotated at the corresponding positions in the graphs. The locations of GC-rich expansion segments are highlighted by light blue rectangles. RNase L cleavage sites are highlighted in red.

    Journal: Nucleic Acids Research

    Article Title: Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs

    doi: 10.1093/nar/gku118

    Figure Lengend Snippet: Endoribonuclease cleavage sites in rRNAs from W12 HeLa cells. RNAs from mock-infected and PV-infected W12 HeLa cells ( Figure 3 B) were used for 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing. The location and frequency of cleavage sites in 28S rRNA ( A ), 18S rRNA ( B ), 5.8S rRNA ( C ) and 5S rRNA ( D ) are shown for mock-infected and PV-infected RNA samples isolated at 8 hpa. X-axis: Nucleotide position of each RNA. Y-axis: Percentage of total UMIs at each cleavage site. Dinucleotides at the 3′-end of abundant RNA fragments are annotated at the corresponding positions in the graphs. The locations of GC-rich expansion segments are highlighted by light blue rectangles. RNase L cleavage sites are highlighted in red.

    Article Snippet: We exploited the 2′, 3′-cyclic phosphates at RNA cleavage sites to make cDNA libraries suitable for Illumina sequencing ( Supplementary Figure S1 ).

    Techniques: Infection, Sequencing, Isolation

    Host and viral RNA from mock-infected and PV-infected HeLa cells. RNA was isolated from mock-infected and PV-infected HeLa cells for 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing. ( A ) PV infection. W12 and M25 HeLa cells were infected with PV using 10 PFUs per cell. PV titers determined by plaque assay and plotted versus time (hpa). ( B ) RNA from PV-infected HeLa cells. RNA was isolated from infected cells, fractionated by agarose gel electrophoresis and visualized using ethidium bromide and UV light. ( C and D ) cDNA reads from W12 (C) and M25 (D) HeLa cells. The RNAs shown in Figure 3 B were used for 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing. Amounts of host and viral cDNA in each sample are plotted (data from Supplementary Table S3 ).

    Journal: Nucleic Acids Research

    Article Title: Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs

    doi: 10.1093/nar/gku118

    Figure Lengend Snippet: Host and viral RNA from mock-infected and PV-infected HeLa cells. RNA was isolated from mock-infected and PV-infected HeLa cells for 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing. ( A ) PV infection. W12 and M25 HeLa cells were infected with PV using 10 PFUs per cell. PV titers determined by plaque assay and plotted versus time (hpa). ( B ) RNA from PV-infected HeLa cells. RNA was isolated from infected cells, fractionated by agarose gel electrophoresis and visualized using ethidium bromide and UV light. ( C and D ) cDNA reads from W12 (C) and M25 (D) HeLa cells. The RNAs shown in Figure 3 B were used for 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing. Amounts of host and viral cDNA in each sample are plotted (data from Supplementary Table S3 ).

    Article Snippet: We exploited the 2′, 3′-cyclic phosphates at RNA cleavage sites to make cDNA libraries suitable for Illumina sequencing ( Supplementary Figure S1 ).

    Techniques: Infection, Isolation, Sequencing, Plaque Assay, Agarose Gel Electrophoresis

    Domains show conservation and expression tendencies. (A) Relationship between gene frequency and AT content in microarrays hybridized with cDNAs obtained from total RNA. (B) Relationship between average FU and AT content in microarrays hybridized with cDNAs obtained from total RNA. A window of 11 genes (average value on the middle one) was applied for FU values. Only coding regions were considered in the AT calculations. (C) Relationship between FU value and AT content in microarrays hybridized with cDNA obtained from total DNA, the median of about 32 microarray spot values was calculated and the mean of medians from two replicates considered. (D) Relationship between the gene lack index and FU. Genes were considered equivalent to R6 counterparts when their polypeptide products shared ≥80% identity over ≥80% of the sequence length in other S. pneumoniae strains with complete genome sequence: 70585, ATCC 700669, CGSP14, D39, G54, Hungary19A-6, JJA, P1031, Taiwan19F-14, TCH8431/19A and TIGR4. An 11-gene window (roughly equivalent to 10 Kb) was applied. Misleading continuum of sharp peaks or poorly defined peaks were obtained when narrower or wider windows were applied, respectively.

    Journal: PLoS ONE

    Article Title: Role of Global and Local Topology in the Regulation of Gene Expression in Streptococcus pneumoniae

    doi: 10.1371/journal.pone.0101574

    Figure Lengend Snippet: Domains show conservation and expression tendencies. (A) Relationship between gene frequency and AT content in microarrays hybridized with cDNAs obtained from total RNA. (B) Relationship between average FU and AT content in microarrays hybridized with cDNAs obtained from total RNA. A window of 11 genes (average value on the middle one) was applied for FU values. Only coding regions were considered in the AT calculations. (C) Relationship between FU value and AT content in microarrays hybridized with cDNA obtained from total DNA, the median of about 32 microarray spot values was calculated and the mean of medians from two replicates considered. (D) Relationship between the gene lack index and FU. Genes were considered equivalent to R6 counterparts when their polypeptide products shared ≥80% identity over ≥80% of the sequence length in other S. pneumoniae strains with complete genome sequence: 70585, ATCC 700669, CGSP14, D39, G54, Hungary19A-6, JJA, P1031, Taiwan19F-14, TCH8431/19A and TIGR4. An 11-gene window (roughly equivalent to 10 Kb) was applied. Misleading continuum of sharp peaks or poorly defined peaks were obtained when narrower or wider windows were applied, respectively.

    Article Snippet: RNA techniques Synthesis of cDNAs from 5 µg of total RNA was performed as previously described . cDNAs obtained were subjected to quantitative qRT-PCR (Chromo 4, BioRad) in 20 µl reactions containing 2 µl of cDNA, 0.4 µM of each specific primer, and 10 µl of LightCycler FastStart Universal A SYBR Green Master (Roche).

    Techniques: Expressing, Microarray, Sequencing