Structured Review

Illumina Inc complementary dna cdna synthesis
Complementary Dna Cdna Synthesis, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/complementary dna cdna synthesis/product/Illumina Inc
Average 91 stars, based on 6 article reviews
Price from $9.99 to $1999.99
complementary dna cdna synthesis - by Bioz Stars, 2020-05
91/100 stars

Images

Related Articles

Amplification:

Article Title: Expression Profile of MicroRNAs and mRNAs in Human Placentas From Pregnancies Complicated by Preeclampsia and Preterm Labor
Article Snippet: .. Following amplification and complementary DNA (cDNA) synthesis, 5 μg of cDNA was reverse, the product was purified, and 20µg of complementary RNA ([cRNA]; 0.5 µg/µl) was fragmented, mixed with 300 µL of hybridization mixture and 200 µl of the mixture was hybridized to HumanRef-12 v3 Expression BeadChip (Illumina, Inc, San Diego, California) consisting of 24,526 oligonucleotide probe sets representing 18,630 transcripts. .. The expression values were background subtracted and globally normalized using BeadStudio version 1.5.1.3 (Illumina) and probes with differential score of ≤13 were independently removed from each cohort.

RNA Sequencing Assay:

Article Title: A Comparison of Selective Pressures in Plant X-Linked and Autosomal Genes
Article Snippet: .. Isolation of messenger RNA (mRNA), complementary DNA (cDNA) synthesis, and high-throughput sequencing were conducted according to the standard Illumina RNA-Seq procedure at the Oxford Genomics Centre of the Wellcome Trust Center for Human Genetics (WTCHG, Oxford, UK). .. High-throughput sequencing for each individual was conducted at WTCHG using an Illumina HiSeq2000 (Illuma INC, San Diego, CA, USA) instrument with 100-base paired-end reads.

High Throughput Screening Assay:

Article Title: A Comparison of Selective Pressures in Plant X-Linked and Autosomal Genes
Article Snippet: .. Isolation of messenger RNA (mRNA), complementary DNA (cDNA) synthesis, and high-throughput sequencing were conducted according to the standard Illumina RNA-Seq procedure at the Oxford Genomics Centre of the Wellcome Trust Center for Human Genetics (WTCHG, Oxford, UK). .. High-throughput sequencing for each individual was conducted at WTCHG using an Illumina HiSeq2000 (Illuma INC, San Diego, CA, USA) instrument with 100-base paired-end reads.

Ligation:

Article Title: Combined cardiomyocyte PKCδ and PKCε gene deletion uncovers their central role in restraining developmental and reactive heart growth
Article Snippet: .. Polyadenylated RNA selection on oligo(dT) Dynabeads, fragmentation, first- and second-strand complementary DNA cDNA synthesis, and ligation of indexed adapters for Illumina sequencing were carried out as previously described ( ). .. Single-end, 50-nucleotide reads were obtained on an Illumina HiSeq 2500; total reads per individual heart sample averaged 23 million, with 59% alignment to the mouse transcriptome defined by the Illumina iGenomes annotation (Ensembl NCBIM37, mm9).

Article Title: Endothelial Notch activation reshapes the angiocrine of sinusoidal endothelia to aggravate liver fibrosis and blunt regeneration in mice
Article Snippet: .. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA), and each sample had the RINe above 7.0. mRNA was isolated and fragmented to approximately 200 base pairs (bp) in length and subjected to complementary DNA (cDNA) synthesis followed by adaptor ligation and enrichment with a low‐cycle PCR using the TruSeq RNA LT/HT Sample Prep Kit (Illumina). .. Purified library products were evaluated using the Agilent 2200 TapeStation and Qubit2.0 (Life Technologies, Carlsbad, CA) and then diluted to 10 pM for cluster generation in situ on the HiSeq3000 pair‐end flow cell followed by sequencing (2 × 150 bp) on HiSeq3000.

Isolation:

Article Title: A Comparison of Selective Pressures in Plant X-Linked and Autosomal Genes
Article Snippet: .. Isolation of messenger RNA (mRNA), complementary DNA (cDNA) synthesis, and high-throughput sequencing were conducted according to the standard Illumina RNA-Seq procedure at the Oxford Genomics Centre of the Wellcome Trust Center for Human Genetics (WTCHG, Oxford, UK). .. High-throughput sequencing for each individual was conducted at WTCHG using an Illumina HiSeq2000 (Illuma INC, San Diego, CA, USA) instrument with 100-base paired-end reads.

Article Title: Endothelial Notch activation reshapes the angiocrine of sinusoidal endothelia to aggravate liver fibrosis and blunt regeneration in mice
Article Snippet: .. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA), and each sample had the RINe above 7.0. mRNA was isolated and fragmented to approximately 200 base pairs (bp) in length and subjected to complementary DNA (cDNA) synthesis followed by adaptor ligation and enrichment with a low‐cycle PCR using the TruSeq RNA LT/HT Sample Prep Kit (Illumina). .. Purified library products were evaluated using the Agilent 2200 TapeStation and Qubit2.0 (Life Technologies, Carlsbad, CA) and then diluted to 10 pM for cluster generation in situ on the HiSeq3000 pair‐end flow cell followed by sequencing (2 × 150 bp) on HiSeq3000.

Purification:

Article Title: Expression Profile of MicroRNAs and mRNAs in Human Placentas From Pregnancies Complicated by Preeclampsia and Preterm Labor
Article Snippet: .. Following amplification and complementary DNA (cDNA) synthesis, 5 μg of cDNA was reverse, the product was purified, and 20µg of complementary RNA ([cRNA]; 0.5 µg/µl) was fragmented, mixed with 300 µL of hybridization mixture and 200 µl of the mixture was hybridized to HumanRef-12 v3 Expression BeadChip (Illumina, Inc, San Diego, California) consisting of 24,526 oligonucleotide probe sets representing 18,630 transcripts. .. The expression values were background subtracted and globally normalized using BeadStudio version 1.5.1.3 (Illumina) and probes with differential score of ≤13 were independently removed from each cohort.

Polymerase Chain Reaction:

Article Title: Endothelial Notch activation reshapes the angiocrine of sinusoidal endothelia to aggravate liver fibrosis and blunt regeneration in mice
Article Snippet: .. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA), and each sample had the RINe above 7.0. mRNA was isolated and fragmented to approximately 200 base pairs (bp) in length and subjected to complementary DNA (cDNA) synthesis followed by adaptor ligation and enrichment with a low‐cycle PCR using the TruSeq RNA LT/HT Sample Prep Kit (Illumina). .. Purified library products were evaluated using the Agilent 2200 TapeStation and Qubit2.0 (Life Technologies, Carlsbad, CA) and then diluted to 10 pM for cluster generation in situ on the HiSeq3000 pair‐end flow cell followed by sequencing (2 × 150 bp) on HiSeq3000.

Selection:

Article Title: Combined cardiomyocyte PKCδ and PKCε gene deletion uncovers their central role in restraining developmental and reactive heart growth
Article Snippet: .. Polyadenylated RNA selection on oligo(dT) Dynabeads, fragmentation, first- and second-strand complementary DNA cDNA synthesis, and ligation of indexed adapters for Illumina sequencing were carried out as previously described ( ). .. Single-end, 50-nucleotide reads were obtained on an Illumina HiSeq 2500; total reads per individual heart sample averaged 23 million, with 59% alignment to the mouse transcriptome defined by the Illumina iGenomes annotation (Ensembl NCBIM37, mm9).

Expressing:

Article Title: Expression Profile of MicroRNAs and mRNAs in Human Placentas From Pregnancies Complicated by Preeclampsia and Preterm Labor
Article Snippet: .. Following amplification and complementary DNA (cDNA) synthesis, 5 μg of cDNA was reverse, the product was purified, and 20µg of complementary RNA ([cRNA]; 0.5 µg/µl) was fragmented, mixed with 300 µL of hybridization mixture and 200 µl of the mixture was hybridized to HumanRef-12 v3 Expression BeadChip (Illumina, Inc, San Diego, California) consisting of 24,526 oligonucleotide probe sets representing 18,630 transcripts. .. The expression values were background subtracted and globally normalized using BeadStudio version 1.5.1.3 (Illumina) and probes with differential score of ≤13 were independently removed from each cohort.

Sequencing:

Article Title: A Comparison of Selective Pressures in Plant X-Linked and Autosomal Genes
Article Snippet: .. Isolation of messenger RNA (mRNA), complementary DNA (cDNA) synthesis, and high-throughput sequencing were conducted according to the standard Illumina RNA-Seq procedure at the Oxford Genomics Centre of the Wellcome Trust Center for Human Genetics (WTCHG, Oxford, UK). .. High-throughput sequencing for each individual was conducted at WTCHG using an Illumina HiSeq2000 (Illuma INC, San Diego, CA, USA) instrument with 100-base paired-end reads.

Article Title: Combined cardiomyocyte PKCδ and PKCε gene deletion uncovers their central role in restraining developmental and reactive heart growth
Article Snippet: .. Polyadenylated RNA selection on oligo(dT) Dynabeads, fragmentation, first- and second-strand complementary DNA cDNA synthesis, and ligation of indexed adapters for Illumina sequencing were carried out as previously described ( ). .. Single-end, 50-nucleotide reads were obtained on an Illumina HiSeq 2500; total reads per individual heart sample averaged 23 million, with 59% alignment to the mouse transcriptome defined by the Illumina iGenomes annotation (Ensembl NCBIM37, mm9).

Article Title: Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat
Article Snippet: .. BGI also conducted complementary DNA (cDNA) synthesis, Illumina library preparation, indexing and library quality control, cluster generation and sequencing using Illumina HiSeq 2000 (single-end, 49 bp). ..

Article Title: Transcriptomic responses of Biomphalaria pfeifferi to Schistosoma mansoni: Investigation of a neglected African snail that supports more S. mansoni transmission than any other snail species
Article Snippet: .. Complementary DNA (cDNA) synthesis and Illumina Hi-Seq sequencing was performed at the National Center for Genome Resources (NCGR) in Santa Fe, NM. .. Most liquid handling was performed by a Sciclone G3 Automated Liquid Handling Workstation (Caliper Life Sciences, Hopkinton MA) with Multi TEC Control (INHECO, Martinsried Germany).

Sample Prep:

Article Title: Endothelial Notch activation reshapes the angiocrine of sinusoidal endothelia to aggravate liver fibrosis and blunt regeneration in mice
Article Snippet: .. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA), and each sample had the RINe above 7.0. mRNA was isolated and fragmented to approximately 200 base pairs (bp) in length and subjected to complementary DNA (cDNA) synthesis followed by adaptor ligation and enrichment with a low‐cycle PCR using the TruSeq RNA LT/HT Sample Prep Kit (Illumina). .. Purified library products were evaluated using the Agilent 2200 TapeStation and Qubit2.0 (Life Technologies, Carlsbad, CA) and then diluted to 10 pM for cluster generation in situ on the HiSeq3000 pair‐end flow cell followed by sequencing (2 × 150 bp) on HiSeq3000.

Hybridization:

Article Title: Expression Profile of MicroRNAs and mRNAs in Human Placentas From Pregnancies Complicated by Preeclampsia and Preterm Labor
Article Snippet: .. Following amplification and complementary DNA (cDNA) synthesis, 5 μg of cDNA was reverse, the product was purified, and 20µg of complementary RNA ([cRNA]; 0.5 µg/µl) was fragmented, mixed with 300 µL of hybridization mixture and 200 µl of the mixture was hybridized to HumanRef-12 v3 Expression BeadChip (Illumina, Inc, San Diego, California) consisting of 24,526 oligonucleotide probe sets representing 18,630 transcripts. .. The expression values were background subtracted and globally normalized using BeadStudio version 1.5.1.3 (Illumina) and probes with differential score of ≤13 were independently removed from each cohort.

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 88
    Illumina Inc cyclic phosphate cdna synthesis
    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′, <t>3′-cyclic</t> 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.
    Cyclic Phosphate Cdna Synthesis, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 22 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cyclic phosphate cdna synthesis/product/Illumina Inc
    Average 88 stars, based on 22 article reviews
    Price from $9.99 to $1999.99
    cyclic phosphate cdna synthesis - by Bioz Stars, 2020-05
    88/100 stars
      Buy from Supplier

    95
    Illumina Inc double stranded cdna
    Methods for total RNA-Seq Shown are the salient details for five protocols for total RNA-Seq. DSN-lite (Duplex-specific nuclease, low C 0 t normalization), RNase H, and <t>Ribo-Zero</t> were tested for low quality samples; SMART was tested for low quantity samples. NuGEN, which generates double-stranded <t>cDNA</t> amplified using Ribo-SPIA (Single Primer Isothermal Amplification), was tested for both types of samples: (NuGEN 100f for low quality; NuGEN 1i for low quantity, and NuGEN 1f for low quantity and low quality). In each case, RNA and matching cDNA are in black, adaptors and primers in color, and rRNA is in grey.
    Double Stranded Cdna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 86 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/double stranded cdna/product/Illumina Inc
    Average 95 stars, based on 86 article reviews
    Price from $9.99 to $1999.99
    double stranded cdna - by Bioz Stars, 2020-05
    95/100 stars
      Buy from Supplier

    90
    Illumina Inc double stranded cdna synthesis
    Fig fruit developmental stages and tissues used to extract <t>RNA</t> and construct <t>cDNA</t> libraries for the Illumina high-throughput sequencing. (A) Developmental stages of parthenocarpic (top rows of each set) and pollinated (lower rows of each set) fruit displaying pulp and inflorescence; 8WAP – 8 weeks after pollination; 9WAP – 9 weeks after pollination; 10% – 10% fruit ripening; 60% – 60% fruit ripening; 100% – 100% fruit ripening. (B) Parthenocarpic sampled tissues that were used in this study. ( C ) Pollinated sampled tissues that were used in this study.
    Double Stranded Cdna Synthesis, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 103 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/double stranded cdna synthesis/product/Illumina Inc
    Average 90 stars, based on 103 article reviews
    Price from $9.99 to $1999.99
    double stranded cdna synthesis - by Bioz Stars, 2020-05
    90/100 stars
      Buy from Supplier

    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 optimized and validated 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A and RNA from uninfected and poliovirus-infected HeLa cells.

    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 optimized and validated 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A and RNA from uninfected and poliovirus-infected HeLa cells.

    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 optimized and validated 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A and RNA from uninfected and poliovirus-infected HeLa cells.

    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 optimized and validated 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A and RNA from uninfected and poliovirus-infected HeLa cells.

    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 optimized and validated 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A and RNA from uninfected and poliovirus-infected HeLa cells.

    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 optimized and validated 2′, 3′-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A and RNA from uninfected and poliovirus-infected HeLa cells.

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

    Methods for total RNA-Seq Shown are the salient details for five protocols for total RNA-Seq. DSN-lite (Duplex-specific nuclease, low C 0 t normalization), RNase H, and Ribo-Zero were tested for low quality samples; SMART was tested for low quantity samples. NuGEN, which generates double-stranded cDNA amplified using Ribo-SPIA (Single Primer Isothermal Amplification), was tested for both types of samples: (NuGEN 100f for low quality; NuGEN 1i for low quantity, and NuGEN 1f for low quantity and low quality). In each case, RNA and matching cDNA are in black, adaptors and primers in color, and rRNA is in grey.

    Journal: Nature methods

    Article Title: Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples

    doi: 10.1038/nmeth.2483

    Figure Lengend Snippet: Methods for total RNA-Seq Shown are the salient details for five protocols for total RNA-Seq. DSN-lite (Duplex-specific nuclease, low C 0 t normalization), RNase H, and Ribo-Zero were tested for low quality samples; SMART was tested for low quantity samples. NuGEN, which generates double-stranded cDNA amplified using Ribo-SPIA (Single Primer Isothermal Amplification), was tested for both types of samples: (NuGEN 100f for low quality; NuGEN 1i for low quantity, and NuGEN 1f for low quantity and low quality). In each case, RNA and matching cDNA are in black, adaptors and primers in color, and rRNA is in grey.

    Article Snippet: For the Ribo-Zero libraries, we synthesized double-stranded cDNA and prepared an indexed Illumina library as described for the RNase H libraries.

    Techniques: RNA Sequencing Assay, Amplification

    Fig fruit developmental stages and tissues used to extract RNA and construct cDNA libraries for the Illumina high-throughput sequencing. (A) Developmental stages of parthenocarpic (top rows of each set) and pollinated (lower rows of each set) fruit displaying pulp and inflorescence; 8WAP – 8 weeks after pollination; 9WAP – 9 weeks after pollination; 10% – 10% fruit ripening; 60% – 60% fruit ripening; 100% – 100% fruit ripening. (B) Parthenocarpic sampled tissues that were used in this study. ( C ) Pollinated sampled tissues that were used in this study.

    Journal: Frontiers in Plant Science

    Article Title: Tissue-Specific Transcriptome and Hormonal Regulation of Pollinated and Parthenocarpic Fig (Ficus carica L.) Fruit Suggest that Fruit Ripening Is Coordinated by the Reproductive Part of the Syconium

    doi: 10.3389/fpls.2016.01696

    Figure Lengend Snippet: Fig fruit developmental stages and tissues used to extract RNA and construct cDNA libraries for the Illumina high-throughput sequencing. (A) Developmental stages of parthenocarpic (top rows of each set) and pollinated (lower rows of each set) fruit displaying pulp and inflorescence; 8WAP – 8 weeks after pollination; 9WAP – 9 weeks after pollination; 10% – 10% fruit ripening; 60% – 60% fruit ripening; 100% – 100% fruit ripening. (B) Parthenocarpic sampled tissues that were used in this study. ( C ) Pollinated sampled tissues that were used in this study.

    Article Snippet: RNA fragmentation, double-stranded cDNA synthesis and adaptor ligation were performed using the TruseqTM RNA Sample Prep Kit-v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

    Techniques: Construct, Next-Generation Sequencing

    OSU-SpARKFuse workflow. After tumor content estimation, RNA is extracted from routine clinical specimens. A total of 250 ng of RNA is used for library construction, including rRNA depletion, cDNA synthesis, and ligation of unique indexed adapters. cDNA libraries are hybridized and captured with 3522 custom probes and sequenced on the Illumina MiSeq. FASTQ files are processed with a customized in-house pipeline to generate alignment metrics and accurately call gene fusions. High-confidence fusion calls are reported. DV 200 , percentage of RNA fragments > 200 nucleotides; ERCC, External RNA Controls Consortium; QC, quality control; RIN e , RNA integrity number equivalent.

    Journal: The Journal of Molecular Diagnostics : JMD

    Article Title: Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors

    doi: 10.1016/j.jmoldx.2017.05.006

    Figure Lengend Snippet: OSU-SpARKFuse workflow. After tumor content estimation, RNA is extracted from routine clinical specimens. A total of 250 ng of RNA is used for library construction, including rRNA depletion, cDNA synthesis, and ligation of unique indexed adapters. cDNA libraries are hybridized and captured with 3522 custom probes and sequenced on the Illumina MiSeq. FASTQ files are processed with a customized in-house pipeline to generate alignment metrics and accurately call gene fusions. High-confidence fusion calls are reported. DV 200 , percentage of RNA fragments > 200 nucleotides; ERCC, External RNA Controls Consortium; QC, quality control; RIN e , RNA integrity number equivalent.

    Article Snippet: Ribo-Zero (Illumina, San Diego, CA) rRNA depletion was performed followed by chemical fragmentation, cDNA synthesis, A-tailing, and ligation of unique sequencing indexes using Illumina TruSeq Stranded Total RNA Library Kit.

    Techniques: Ligation