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Illumina Inc human oligonucleotides
Human Oligonucleotides, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/human oligonucleotides/product/Illumina Inc
Average 79 stars, based on 1 article reviews
Price from $9.99 to $1999.99
human oligonucleotides - by Bioz Stars, 2020-04
79/100 stars

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Microarray:

Article Title: Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus
Article Snippet: .. Microarray hybridization and scanning The labeled product was re-suspended in 40 μL hybridization buffer (40% deionised formamide, 5 × SSC, 5 × Denhart's, 1 mM Na Pyrophosphate, 50 mM Tris Ph 7.4 and 0.1%SDS) and hybridized onto a microarray slide containing 23,000 human oligonucleotides (Illumina Inc. San Diego), printed in-house on to Codelink slides using a BioRobotics Microgrid II arrayer. .. After over-night hybridization of the slides at 48°C in a water bath, they were washed in 2 × SSC, 0.1 × SSC, 0.05% Tween 20, and 0.1 × SSC sequentially for 5 min each and scanned using an Axon 40001A scanner.

Hybridization:

Article Title: Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus
Article Snippet: .. Microarray hybridization and scanning The labeled product was re-suspended in 40 μL hybridization buffer (40% deionised formamide, 5 × SSC, 5 × Denhart's, 1 mM Na Pyrophosphate, 50 mM Tris Ph 7.4 and 0.1%SDS) and hybridized onto a microarray slide containing 23,000 human oligonucleotides (Illumina Inc. San Diego), printed in-house on to Codelink slides using a BioRobotics Microgrid II arrayer. .. After over-night hybridization of the slides at 48°C in a water bath, they were washed in 2 × SSC, 0.1 × SSC, 0.05% Tween 20, and 0.1 × SSC sequentially for 5 min each and scanned using an Axon 40001A scanner.

Labeling:

Article Title: Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus
Article Snippet: .. Microarray hybridization and scanning The labeled product was re-suspended in 40 μL hybridization buffer (40% deionised formamide, 5 × SSC, 5 × Denhart's, 1 mM Na Pyrophosphate, 50 mM Tris Ph 7.4 and 0.1%SDS) and hybridized onto a microarray slide containing 23,000 human oligonucleotides (Illumina Inc. San Diego), printed in-house on to Codelink slides using a BioRobotics Microgrid II arrayer. .. After over-night hybridization of the slides at 48°C in a water bath, they were washed in 2 × SSC, 0.1 × SSC, 0.05% Tween 20, and 0.1 × SSC sequentially for 5 min each and scanned using an Axon 40001A scanner.

Software:

Article Title: Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus
Article Snippet: Microarray hybridization and scanning The labeled product was re-suspended in 40 μL hybridization buffer (40% deionised formamide, 5 × SSC, 5 × Denhart's, 1 mM Na Pyrophosphate, 50 mM Tris Ph 7.4 and 0.1%SDS) and hybridized onto a microarray slide containing 23,000 human oligonucleotides (Illumina Inc. San Diego), printed in-house on to Codelink slides using a BioRobotics Microgrid II arrayer. .. Signal quantification was performed using Bluefuse software (2.0) (BlueGnome, Cambridge, UK).

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  • 93
    Illumina Inc earth microbiome project primer set
    Early HMOS dietary intervention changes the alpha diversity and beta diversity of fecal <t>microbiota</t> of the non-diabetic and diabetic mice within each group at four collection points. ( A ) richness. ( B ) Shannon’s index. ( C ) Simpson’s index. ( D ) evenness. Alpha diversity indices data are represented as mean ± SEM, n = 17–20/ group, *p
    Earth Microbiome Project Primer Set, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/earth microbiome project primer set/product/Illumina Inc
    Average 93 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    earth microbiome project primer set - by Bioz Stars, 2020-04
    93/100 stars
      Buy from Supplier

    97
    Illumina Inc human transcriptome
    The human muscle non-coding RNA <t>transcriptome:</t> relationship with insulin sensitivity . ( A ) The non-competitive nature of RNA quantification and tissue configured CDF for the HTA 2.0 microarray facilitated the first detailed and quantitative view of long non-coding RNA molecule expression in human skeletal muscle in vivo ( > 20 000 ENST representing 16 223 genes (ENSG)). The majority of non-coding RNAs (ncRNAs) identified in human muscle were classed as either ‘anti-sense’ molecules or long non-coding RNA (lncRNA). ( B ) We utilized three clinical cohorts ( n = 282), with varying ranges of chronological age, to examine which ncRNAs were related to insulin sensitivity (IS). Eighty-six long ncRNA associated with IS, the majority ( 43 ) being either antisense or lncRNA (Figure 2B , See Supplemental data S3 ). The vast majority of these were also expressed in adipose and pancreatic cells ( in vitro beta cells, Supplemental data S3 ) indicating they could influence insulin biology across multiple organs. The relationship between each ncRNA and IS was largely consistent in the three sub-groups, with greater variability noted among the oldest subjects, which may reflect population stratification ( 62 ). LncRNAs like NEAT1 and MALAT1 were very highly expressed and regulate gene expression via interactions with chromatin ( 139 ), while the majority of the IS related ncRNAs were expressed at a level similar to coding mRNA. ( C ) Four examples of lncRNA molecules related to fasting IS and how they co-vary with their cis expressed protein-coding transcript in vivo ( n = 191, younger samples). The protein-coding transcripts were not themselves significantly correlated with IS. ( D ) Human HepG2 cells (hepatocellular carcinoma cell line) were transfected with 20 nM of phosphorothioate antisense oligonucleotides (PS ASO, one control ASO and four different ASO targeting PRKCQ-AS1 ) in triplicates, and expression of PRKCQ-AS1 (A) and PRKCQ (B) was measured by quantitative real-time PCR. ASO-induced knockdown was statistically significant ( P
    Human Transcriptome, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 97/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/human transcriptome/product/Illumina Inc
    Average 97 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    human transcriptome - by Bioz Stars, 2020-04
    97/100 stars
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    85
    Illumina Inc sequencing methods rnase l
    Viral RNA fragments produced by <t>RNase</t> 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.
    Sequencing Methods Rnase L, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sequencing methods rnase l/product/Illumina Inc
    Average 85 stars, based on 1 article reviews
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    86
    Illumina Inc rnase l cleavage sites
    Viral RNA fragments produced by <t>RNase</t> 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.
    Rnase L Cleavage Sites, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rnase l cleavage sites/product/Illumina Inc
    Average 86 stars, based on 2 article reviews
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    Image Search Results


    Early HMOS dietary intervention changes the alpha diversity and beta diversity of fecal microbiota of the non-diabetic and diabetic mice within each group at four collection points. ( A ) richness. ( B ) Shannon’s index. ( C ) Simpson’s index. ( D ) evenness. Alpha diversity indices data are represented as mean ± SEM, n = 17–20/ group, *p

    Journal: Scientific Reports

    Article Title: Human milk oligosaccharides protect against the development of autoimmune diabetes in NOD-mice

    doi: 10.1038/s41598-018-22052-y

    Figure Lengend Snippet: Early HMOS dietary intervention changes the alpha diversity and beta diversity of fecal microbiota of the non-diabetic and diabetic mice within each group at four collection points. ( A ) richness. ( B ) Shannon’s index. ( C ) Simpson’s index. ( D ) evenness. Alpha diversity indices data are represented as mean ± SEM, n = 17–20/ group, *p

    Article Snippet: Total DNA was extracted from NOD-mice fecal samples (FastDNA bead-beating Spin Kit for Soil, MP Biomedicals, Solon, OH), amplified the V4 variable region of the microbial 16 S rRNA gene (Earth Microbiome Project primer set, adapted for the Illumina platform) , and sequenced on an Illumina MiSeq (2 × 151 bp reads) at Argonne National Laboratory.

    Techniques: Mouse Assay

    Early HMOS dietary intervention alters fecal microbiota composition over time. Fecal samples at Wk4 (baseline), Wk9 (start intervention), Wk14 (post-intervention) and Wk30 (endpoint) were analyzed using 16 S rRNA. ( A ) Phylum level pie charts, organized by weekly collection time points, significance indicated either by: ( # )False Discovery Rate (FDR) p

    Journal: Scientific Reports

    Article Title: Human milk oligosaccharides protect against the development of autoimmune diabetes in NOD-mice

    doi: 10.1038/s41598-018-22052-y

    Figure Lengend Snippet: Early HMOS dietary intervention alters fecal microbiota composition over time. Fecal samples at Wk4 (baseline), Wk9 (start intervention), Wk14 (post-intervention) and Wk30 (endpoint) were analyzed using 16 S rRNA. ( A ) Phylum level pie charts, organized by weekly collection time points, significance indicated either by: ( # )False Discovery Rate (FDR) p

    Article Snippet: Total DNA was extracted from NOD-mice fecal samples (FastDNA bead-beating Spin Kit for Soil, MP Biomedicals, Solon, OH), amplified the V4 variable region of the microbial 16 S rRNA gene (Earth Microbiome Project primer set, adapted for the Illumina platform) , and sequenced on an Illumina MiSeq (2 × 151 bp reads) at Argonne National Laboratory.

    Techniques:

    The human muscle non-coding RNA transcriptome: relationship with insulin sensitivity . ( A ) The non-competitive nature of RNA quantification and tissue configured CDF for the HTA 2.0 microarray facilitated the first detailed and quantitative view of long non-coding RNA molecule expression in human skeletal muscle in vivo ( > 20 000 ENST representing 16 223 genes (ENSG)). The majority of non-coding RNAs (ncRNAs) identified in human muscle were classed as either ‘anti-sense’ molecules or long non-coding RNA (lncRNA). ( B ) We utilized three clinical cohorts ( n = 282), with varying ranges of chronological age, to examine which ncRNAs were related to insulin sensitivity (IS). Eighty-six long ncRNA associated with IS, the majority ( 43 ) being either antisense or lncRNA (Figure 2B , See Supplemental data S3 ). The vast majority of these were also expressed in adipose and pancreatic cells ( in vitro beta cells, Supplemental data S3 ) indicating they could influence insulin biology across multiple organs. The relationship between each ncRNA and IS was largely consistent in the three sub-groups, with greater variability noted among the oldest subjects, which may reflect population stratification ( 62 ). LncRNAs like NEAT1 and MALAT1 were very highly expressed and regulate gene expression via interactions with chromatin ( 139 ), while the majority of the IS related ncRNAs were expressed at a level similar to coding mRNA. ( C ) Four examples of lncRNA molecules related to fasting IS and how they co-vary with their cis expressed protein-coding transcript in vivo ( n = 191, younger samples). The protein-coding transcripts were not themselves significantly correlated with IS. ( D ) Human HepG2 cells (hepatocellular carcinoma cell line) were transfected with 20 nM of phosphorothioate antisense oligonucleotides (PS ASO, one control ASO and four different ASO targeting PRKCQ-AS1 ) in triplicates, and expression of PRKCQ-AS1 (A) and PRKCQ (B) was measured by quantitative real-time PCR. ASO-induced knockdown was statistically significant ( P

    Journal: Nucleic Acids Research

    Article Title: A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease

    doi: 10.1093/nar/gky570

    Figure Lengend Snippet: The human muscle non-coding RNA transcriptome: relationship with insulin sensitivity . ( A ) The non-competitive nature of RNA quantification and tissue configured CDF for the HTA 2.0 microarray facilitated the first detailed and quantitative view of long non-coding RNA molecule expression in human skeletal muscle in vivo ( > 20 000 ENST representing 16 223 genes (ENSG)). The majority of non-coding RNAs (ncRNAs) identified in human muscle were classed as either ‘anti-sense’ molecules or long non-coding RNA (lncRNA). ( B ) We utilized three clinical cohorts ( n = 282), with varying ranges of chronological age, to examine which ncRNAs were related to insulin sensitivity (IS). Eighty-six long ncRNA associated with IS, the majority ( 43 ) being either antisense or lncRNA (Figure 2B , See Supplemental data S3 ). The vast majority of these were also expressed in adipose and pancreatic cells ( in vitro beta cells, Supplemental data S3 ) indicating they could influence insulin biology across multiple organs. The relationship between each ncRNA and IS was largely consistent in the three sub-groups, with greater variability noted among the oldest subjects, which may reflect population stratification ( 62 ). LncRNAs like NEAT1 and MALAT1 were very highly expressed and regulate gene expression via interactions with chromatin ( 139 ), while the majority of the IS related ncRNAs were expressed at a level similar to coding mRNA. ( C ) Four examples of lncRNA molecules related to fasting IS and how they co-vary with their cis expressed protein-coding transcript in vivo ( n = 191, younger samples). The protein-coding transcripts were not themselves significantly correlated with IS. ( D ) Human HepG2 cells (hepatocellular carcinoma cell line) were transfected with 20 nM of phosphorothioate antisense oligonucleotides (PS ASO, one control ASO and four different ASO targeting PRKCQ-AS1 ) in triplicates, and expression of PRKCQ-AS1 (A) and PRKCQ (B) was measured by quantitative real-time PCR. ASO-induced knockdown was statistically significant ( P

    Article Snippet: Thus, while there are clearly further methodological factors to consider before we have a definitive view on the human transcriptome, the present analysis indicates that current representations of the ncRNA transcriptome by the Illumina Human BodyMap and GTEx are far from comprehensive, with reported tissue specific expression patterns being inaccurate.

    Techniques: Microarray, Expressing, In Vivo, In Vitro, Transfection, Allele-specific Oligonucleotide, Real-time Polymerase Chain Reaction

    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: 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods RNase L, RNase A and other metal-ion–independent endoribonucleases target single-stranded regions of RNA, leaving 2′, 3′-cyclic phosphates at the end of RNA fragments ( ).

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

    Cleavage sites mapped onto rRNA secondary and tertiary structures. Secondary and tertiary structures from Anger et al. ( 42 ). ( A ) RNase L cleavage sites in 18S rRNA secondary structure. Portion of 18S rRNA structure highlighting the location of RNase L cleavage sites. ( B ) Location of RNase L cleavage sites in 80S ribosome tertiary structure. RNase L-dependent cleavage sites highlighted in red spheres. ( C ) 3′-end of 5.8S and 5S rRNAs. 3′-end of 5.8S and 5S rRNAs highlighted in orange spheres. ( D ) RNase L-independent cleavage sites. Some representative RNase L-independent cleavage sites highlighted in yellow spheres.

    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: Cleavage sites mapped onto rRNA secondary and tertiary structures. Secondary and tertiary structures from Anger et al. ( 42 ). ( A ) RNase L cleavage sites in 18S rRNA secondary structure. Portion of 18S rRNA structure highlighting the location of RNase L cleavage sites. ( B ) Location of RNase L cleavage sites in 80S ribosome tertiary structure. RNase L-dependent cleavage sites highlighted in red spheres. ( C ) 3′-end of 5.8S and 5S rRNAs. 3′-end of 5.8S and 5S rRNAs highlighted in orange spheres. ( D ) RNase L-independent cleavage sites. Some representative RNase L-independent cleavage sites highlighted in yellow spheres.

    Article Snippet: 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods RNase L, RNase A and other metal-ion–independent endoribonucleases target single-stranded regions of RNA, leaving 2′, 3′-cyclic phosphates at the end of RNA fragments ( ).

    Techniques:

    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: 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods RNase L, RNase A and other metal-ion–independent endoribonucleases target single-stranded regions of RNA, leaving 2′, 3′-cyclic phosphates at the end of RNA fragments ( ).

    Techniques: Infection, Sequencing, Isolation

    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: In contrast, quantitative analyses of RNase L cleavage sites in HCV RNA using 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing are extremely precise.

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

    Cleavage sites mapped onto rRNA secondary and tertiary structures. Secondary and tertiary structures from Anger et al. ( 42 ). ( A ) RNase L cleavage sites in 18S rRNA secondary structure. Portion of 18S rRNA structure highlighting the location of RNase L cleavage sites. ( B ) Location of RNase L cleavage sites in 80S ribosome tertiary structure. RNase L-dependent cleavage sites highlighted in red spheres. ( C ) 3′-end of 5.8S and 5S rRNAs. 3′-end of 5.8S and 5S rRNAs highlighted in orange spheres. ( D ) RNase L-independent cleavage sites. Some representative RNase L-independent cleavage sites highlighted in yellow spheres.

    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: Cleavage sites mapped onto rRNA secondary and tertiary structures. Secondary and tertiary structures from Anger et al. ( 42 ). ( A ) RNase L cleavage sites in 18S rRNA secondary structure. Portion of 18S rRNA structure highlighting the location of RNase L cleavage sites. ( B ) Location of RNase L cleavage sites in 80S ribosome tertiary structure. RNase L-dependent cleavage sites highlighted in red spheres. ( C ) 3′-end of 5.8S and 5S rRNAs. 3′-end of 5.8S and 5S rRNAs highlighted in orange spheres. ( D ) RNase L-independent cleavage sites. Some representative RNase L-independent cleavage sites highlighted in yellow spheres.

    Article Snippet: In contrast, quantitative analyses of RNase L cleavage sites in HCV RNA using 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing are extremely precise.

    Techniques:

    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: In contrast, quantitative analyses of RNase L cleavage sites in HCV RNA using 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing are extremely precise.

    Techniques: Infection, Sequencing, Isolation