ribominus eukaryote system v2 Thermo Fisher Search Results


  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 99
    Thermo Fisher ribominus eukaryote system v2
    Ribominus Eukaryote System V2, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 351 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ribominus eukaryote system v2/product/Thermo Fisher
    Average 99 stars, based on 351 article reviews
    Price from $9.99 to $1999.99
    ribominus eukaryote system v2 - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    89
    Thermo Fisher ribominus eukaryote kit v2
    Schematic representation of the method. A . Library preparation, starting from deprived ribosomal fraction of total RNA. The two strand-specific tags, rv5-3 and complementary fw5-3 tag (respectively in grey and black) are represented. a) Synthesis of the 1 st cDNA strand, using the Tag-random-octamer primer rv5-3tag. b) 1 st strand cDNAs ligation. c) Synthesis of the 2 nd cDNA strand with random primers and Phi29 DNA polymerase amplification. This step produced the fw5-3 tag. d) Mapping of the reads using strand-specific tags to correctly assign reads onto the genome. If the gene x is on the positive strand (+) of the genome, whereas the gene y on the negative strand (-), reads tagged with fw5-3 tag map gene x on strand + and gene y on strand -. Conversely rv5-3 tagged reads map an opposite orientation in the same locus. B . Removal of ribosomal RNAs from total RNAs. Efficiency of rRNA depletion was evaluated by means of an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit. Both in the OST-78 and in the OST-83 samples, a dramatic reduction in 18S and 28S rRNA bands compared to the <t>pre-Ribominus</t> samples was confirmed. C . OST-78 and OST-83 RNA samples were retro-transcribed, ligated and amplified with the Phi29 DNA polymerase. After 4 h amplification, we obtained DNA fragments of high molecular weight (about 23 kb) visualized on 1% agarose gel.
    Ribominus Eukaryote Kit V2, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 334 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ribominus eukaryote kit v2/product/Thermo Fisher
    Average 89 stars, based on 334 article reviews
    Price from $9.99 to $1999.99
    ribominus eukaryote kit v2 - by Bioz Stars, 2020-09
    89/100 stars
      Buy from Supplier

    98
    Thermo Fisher low input ribominus eukaryote system v2
    Identification of SARS-Cov-2 through nasopharyngeal swab metatranscriptomics. A) Left panel: extraction of RNA from nasopharyngeal swab was performed according to a protocol validated in our laboratory (COVID-19 Extraction and Amplification with Maxwell® 16 Viral Total Nucleic Acid and GoTaq® Probe 1-Step RT-qPCR; Application Report, Promega 2020). Total RNA sequencing after rRNA depletion followed the protocol of the Ion Total RNA-Seq kit v2, in the Ion S5 platform. Depletion of human ribosomal RNA was done with the Low Input <t>RiboMinus™</t> Eukaryote <t>System</t> v2 kit. Right panel: raw reads were submitted to quality filter where reads larger than 30 nt with Phred quality > 20 were aligned into human reference genome. Unaligned reads were used to perform contig assemblage. Assembled contigs were compared to NCBI databases using Blast software. Contigs that presented sequence similarity to SARS-Cov2-2 with e-value lower than 1e-5 were considered as from viral origin. Viral contigs were further submitted to contig extension using SPAdes and ‘trusted contigs’ option that was followed by cap3 tool to remove sequence redundancy. B) SARS-Cov-2 coverage profile of reads and assembled contigs. Reads were normalized by number of reads from each library. Contigs in red indicate high quality contigs larger than 400 nt with coverage of reads in both libraries.
    Low Input Ribominus Eukaryote System V2, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 98/100, based on 84 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/low input ribominus eukaryote system v2/product/Thermo Fisher
    Average 98 stars, based on 84 article reviews
    Price from $9.99 to $1999.99
    low input ribominus eukaryote system v2 - by Bioz Stars, 2020-09
    98/100 stars
      Buy from Supplier

    Image Search Results


    Schematic representation of the method. A . Library preparation, starting from deprived ribosomal fraction of total RNA. The two strand-specific tags, rv5-3 and complementary fw5-3 tag (respectively in grey and black) are represented. a) Synthesis of the 1 st cDNA strand, using the Tag-random-octamer primer rv5-3tag. b) 1 st strand cDNAs ligation. c) Synthesis of the 2 nd cDNA strand with random primers and Phi29 DNA polymerase amplification. This step produced the fw5-3 tag. d) Mapping of the reads using strand-specific tags to correctly assign reads onto the genome. If the gene x is on the positive strand (+) of the genome, whereas the gene y on the negative strand (-), reads tagged with fw5-3 tag map gene x on strand + and gene y on strand -. Conversely rv5-3 tagged reads map an opposite orientation in the same locus. B . Removal of ribosomal RNAs from total RNAs. Efficiency of rRNA depletion was evaluated by means of an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit. Both in the OST-78 and in the OST-83 samples, a dramatic reduction in 18S and 28S rRNA bands compared to the pre-Ribominus samples was confirmed. C . OST-78 and OST-83 RNA samples were retro-transcribed, ligated and amplified with the Phi29 DNA polymerase. After 4 h amplification, we obtained DNA fragments of high molecular weight (about 23 kb) visualized on 1% agarose gel.

    Journal: BMC Genomics

    Article Title: A platform independent RNA-Seq protocol for the detection of transcriptome complexity

    doi: 10.1186/1471-2164-14-855

    Figure Lengend Snippet: Schematic representation of the method. A . Library preparation, starting from deprived ribosomal fraction of total RNA. The two strand-specific tags, rv5-3 and complementary fw5-3 tag (respectively in grey and black) are represented. a) Synthesis of the 1 st cDNA strand, using the Tag-random-octamer primer rv5-3tag. b) 1 st strand cDNAs ligation. c) Synthesis of the 2 nd cDNA strand with random primers and Phi29 DNA polymerase amplification. This step produced the fw5-3 tag. d) Mapping of the reads using strand-specific tags to correctly assign reads onto the genome. If the gene x is on the positive strand (+) of the genome, whereas the gene y on the negative strand (-), reads tagged with fw5-3 tag map gene x on strand + and gene y on strand -. Conversely rv5-3 tagged reads map an opposite orientation in the same locus. B . Removal of ribosomal RNAs from total RNAs. Efficiency of rRNA depletion was evaluated by means of an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit. Both in the OST-78 and in the OST-83 samples, a dramatic reduction in 18S and 28S rRNA bands compared to the pre-Ribominus samples was confirmed. C . OST-78 and OST-83 RNA samples were retro-transcribed, ligated and amplified with the Phi29 DNA polymerase. After 4 h amplification, we obtained DNA fragments of high molecular weight (about 23 kb) visualized on 1% agarose gel.

    Article Snippet: The removal of the ribosomal component from the total RNA was performed using the RiboMinus Eukaryote Kit for RNA Seq (Invitrogen), according to the manufacturer’s instructions.

    Techniques: Ligation, Amplification, Produced, Molecular Weight, Agarose Gel Electrophoresis

    Identification of SARS-Cov-2 through nasopharyngeal swab metatranscriptomics. A) Left panel: extraction of RNA from nasopharyngeal swab was performed according to a protocol validated in our laboratory (COVID-19 Extraction and Amplification with Maxwell® 16 Viral Total Nucleic Acid and GoTaq® Probe 1-Step RT-qPCR; Application Report, Promega 2020). Total RNA sequencing after rRNA depletion followed the protocol of the Ion Total RNA-Seq kit v2, in the Ion S5 platform. Depletion of human ribosomal RNA was done with the Low Input RiboMinus™ Eukaryote System v2 kit. Right panel: raw reads were submitted to quality filter where reads larger than 30 nt with Phred quality > 20 were aligned into human reference genome. Unaligned reads were used to perform contig assemblage. Assembled contigs were compared to NCBI databases using Blast software. Contigs that presented sequence similarity to SARS-Cov2-2 with e-value lower than 1e-5 were considered as from viral origin. Viral contigs were further submitted to contig extension using SPAdes and ‘trusted contigs’ option that was followed by cap3 tool to remove sequence redundancy. B) SARS-Cov-2 coverage profile of reads and assembled contigs. Reads were normalized by number of reads from each library. Contigs in red indicate high quality contigs larger than 400 nt with coverage of reads in both libraries.

    Journal: Journal of Virological Methods

    Article Title: Ion torrent-based nasopharyngeal swab metatranscriptomics in COVID-19

    doi: 10.1016/j.jviromet.2020.113888

    Figure Lengend Snippet: Identification of SARS-Cov-2 through nasopharyngeal swab metatranscriptomics. A) Left panel: extraction of RNA from nasopharyngeal swab was performed according to a protocol validated in our laboratory (COVID-19 Extraction and Amplification with Maxwell® 16 Viral Total Nucleic Acid and GoTaq® Probe 1-Step RT-qPCR; Application Report, Promega 2020). Total RNA sequencing after rRNA depletion followed the protocol of the Ion Total RNA-Seq kit v2, in the Ion S5 platform. Depletion of human ribosomal RNA was done with the Low Input RiboMinus™ Eukaryote System v2 kit. Right panel: raw reads were submitted to quality filter where reads larger than 30 nt with Phred quality > 20 were aligned into human reference genome. Unaligned reads were used to perform contig assemblage. Assembled contigs were compared to NCBI databases using Blast software. Contigs that presented sequence similarity to SARS-Cov2-2 with e-value lower than 1e-5 were considered as from viral origin. Viral contigs were further submitted to contig extension using SPAdes and ‘trusted contigs’ option that was followed by cap3 tool to remove sequence redundancy. B) SARS-Cov-2 coverage profile of reads and assembled contigs. Reads were normalized by number of reads from each library. Contigs in red indicate high quality contigs larger than 400 nt with coverage of reads in both libraries.

    Article Snippet: One sample was previously processed with the Low Input RiboMinus™ Eukaryote System v2 (ThermoFisher), for depletion of human ribosomal RNA from total RNA ( ).

    Techniques: Amplification, Quantitative RT-PCR, RNA Sequencing Assay, Software, Sequencing