sirna deep sequencing  (Fasteris Life)

Journal: Molecular therapy. Nucleic acids

Article Title: Deep Sequencing Analyses of DsiRNAs Reveal the Influence of 3′ Terminal Overhangs on Dicing Polarity, Strand Selectivity, and RNA Editing of siRNAs

doi: 10.1038/mtna.2012.6

Figure Lengend Snippet: Illumina Deep sequence analyses and IC 50 values of asymmetric 27-mer TNPO3 Dicer-substrate siRNAs (group II)

Article Snippet: Illumina Deep sequence analyses of asymmetric 27-mer hnRNP H1 Dicer-substrate siRNAs.

Techniques: Sequencing

Journal: Molecular therapy. Nucleic acids

Article Title: Deep Sequencing Analyses of DsiRNAs Reveal the Influence of 3′ Terminal Overhangs on Dicing Polarity, Strand Selectivity, and RNA Editing of siRNAs

doi: 10.1038/mtna.2012.6

Figure Lengend Snippet: Illumina Deep sequence analyses of asymmetric 27-mer Homo sapiens transportin 3 ( TNPO3 ) Dicer-substrate siRNAs (group II). HEK 293 cells were transfected with 10 nmol/l of the asymmetric group II RNA duplexes. Forty hours post-transfection the total RNAs were isolated and prepared for Illumina Deep sequencing. The data collection and alignment are described in Materials and Methods section. ( a ) The total reads and abundance of sense and antisense strands from each duplex. ( b ) The strand distribution was calculated as the ratio of the abundance of antisense to sense. The ratio of antisense (AS) to sense (S) is ranked by the 3′ overhang GG > GC, AA > CC, UU ≫ tt. ( c ) The dicing pattern L-R and R-L are as previously described. The L-R pattern generates the desired siRNA species for target knockdown. Total reads from the top 10 antisense strands and the abundance of L-R cleavage products from the antisense strand. ( d ) Two types of RNA editing: trimming of the 3′ end and post-transcriptional addition of nucleotides at the 3′ or 5′ ends.

Article Snippet: Illumina Deep sequence analyses of asymmetric 27-mer hnRNP H1 Dicer-substrate siRNAs.

Techniques: Sequencing, Transfection, Isolation, Knockdown

Journal: Molecular therapy. Nucleic acids

Article Title: Deep Sequencing Analyses of DsiRNAs Reveal the Influence of 3′ Terminal Overhangs on Dicing Polarity, Strand Selectivity, and RNA Editing of siRNAs

doi: 10.1038/mtna.2012.6

Figure Lengend Snippet: Illumina Deep sequence analyses of asymmetric 27-mer heterogeneous nuclear ribonucleoprotein H ( hnRNP H1 ) Dicer-substrate small interfering RNA (siRNAs). The data collection and alignment were as described above. ( a ) Total reads of the top 10 sense and antisense strands from each duplex. ( b ) The strand distribution was calculated as the ratio of the abundance of antisense to sense. Ratio of antisense (AS) to sense (S) is ranked by the 3′ overhang GG > AA in site 324 Dicer-substrate small interfering RNAs (DsiRNAs) and GG > CC in site 325 DsiRNAs. ( c ) The dicing pattern L-R and R-L are as previously described. The L-R model generates the desired siRNA species for target knockdown. The total reads of the top 10 antisense strands and the abundance of L-R cleavage products are presented.

Article Snippet: Illumina Deep sequence analyses of asymmetric 27-mer hnRNP H1 Dicer-substrate siRNAs.

Techniques: Sequencing, Small Interfering RNA, Knockdown

Journal: Molecular therapy. Nucleic acids

Article Title: Deep Sequencing Analyses of DsiRNAs Reveal the Influence of 3′ Terminal Overhangs on Dicing Polarity, Strand Selectivity, and RNA Editing of siRNAs

doi: 10.1038/mtna.2012.6

Figure Lengend Snippet: Illumina Deep sequence analyses and IC 50 values of asymmetric 27-mer TNPO3 Dicer-substrate siRNAs (group II)

Article Snippet: Illumina Deep sequence analysis of asymmetric TNPO3 27-mer Dicer-substrate siRNAs (group II).

Techniques: Sequencing

Journal: Molecular therapy. Nucleic acids

Article Title: Deep Sequencing Analyses of DsiRNAs Reveal the Influence of 3′ Terminal Overhangs on Dicing Polarity, Strand Selectivity, and RNA Editing of siRNAs

doi: 10.1038/mtna.2012.6

Figure Lengend Snippet: Illumina Deep sequence analyses of asymmetric 27-mer Homo sapiens transportin 3 ( TNPO3 ) Dicer-substrate siRNAs (group II). HEK 293 cells were transfected with 10 nmol/l of the asymmetric group II RNA duplexes. Forty hours post-transfection the total RNAs were isolated and prepared for Illumina Deep sequencing. The data collection and alignment are described in Materials and Methods section. ( a ) The total reads and abundance of sense and antisense strands from each duplex. ( b ) The strand distribution was calculated as the ratio of the abundance of antisense to sense. The ratio of antisense (AS) to sense (S) is ranked by the 3′ overhang GG > GC, AA > CC, UU ≫ tt. ( c ) The dicing pattern L-R and R-L are as previously described. The L-R pattern generates the desired siRNA species for target knockdown. Total reads from the top 10 antisense strands and the abundance of L-R cleavage products from the antisense strand. ( d ) Two types of RNA editing: trimming of the 3′ end and post-transcriptional addition of nucleotides at the 3′ or 5′ ends.

Article Snippet: Illumina Deep sequence analysis of asymmetric TNPO3 27-mer Dicer-substrate siRNAs (group II).

Techniques: Sequencing, Transfection, Isolation, Knockdown

Journal: Molecular therapy. Nucleic acids

Article Title: Deep Sequencing Analyses of DsiRNAs Reveal the Influence of 3′ Terminal Overhangs on Dicing Polarity, Strand Selectivity, and RNA Editing of siRNAs

doi: 10.1038/mtna.2012.6

Figure Lengend Snippet: Illumina Deep sequence analyses of asymmetric 27-mer heterogeneous nuclear ribonucleoprotein H ( hnRNP H1 ) Dicer-substrate small interfering RNA (siRNAs). The data collection and alignment were as described above. ( a ) Total reads of the top 10 sense and antisense strands from each duplex. ( b ) The strand distribution was calculated as the ratio of the abundance of antisense to sense. Ratio of antisense (AS) to sense (S) is ranked by the 3′ overhang GG > AA in site 324 Dicer-substrate small interfering RNAs (DsiRNAs) and GG > CC in site 325 DsiRNAs. ( c ) The dicing pattern L-R and R-L are as previously described. The L-R model generates the desired siRNA species for target knockdown. The total reads of the top 10 antisense strands and the abundance of L-R cleavage products are presented.

Article Snippet: Illumina Deep sequence analysis of asymmetric TNPO3 27-mer Dicer-substrate siRNAs (group II).

Techniques: Sequencing, Small Interfering RNA, Knockdown