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Illumina Inc hiseq2000 system
Hiseq2000 System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 2110 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/hiseq2000 system/product/Illumina Inc
Average 94 stars, based on 2110 article reviews
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hiseq2000 system - by Bioz Stars, 2020-04
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Amplification:

Article Title: High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli
Article Snippet: Illumina Deep Sequencing The sample preparation was performed using the Illumina DNA sample preparation kit, according to the manufacturer's instruction (New England Biolabs). .. Subsequently, adapters designed for library construction were ligated to the PCR fragments, ligation products were gel-purified to select for ∼180–300-bp fragments, and PCR amplification was performed to enrich for the ligated fragments.

Article Title: Somatic mtDNA variation is an important component of Parkinson's disease
Article Snippet: .. 2.3 MtDNA sequencing Pooled amplicons were “tagmented,” amplified, cleaned, normalized, and pooled into 48 sample multiplexes using the Illumina Nextera XT DNA sample preparation kit (Illumina, CA, USA). .. Multiplex pools were sequenced using MiSeq Reagent Kit v3.0 (Illumina, CA, USA) in paired-end, 250 bp reads.

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively. .. The double-strand cDNA was performed followed by PCR amplification.

Article Title: Exome Sequencing Identifies a Missense Variant in EFEMP1 Co-Segregating in a Family with Autosomal Dominant Primary Open-Angle Glaucoma
Article Snippet: Following denaturation (95°C, 5 min), amplified DNA-fragment libraries (~500 ng) were hybridized in-solution under high stringency (65°C, 24 hr) with biotinylated RNA capture probes (~120 bp). .. Captured DNA was eluted (NaOH) and then subject to flow-cell massively-parallel sequencing on a HiSeq2000 System (Illumina, San Diego, CA) using the Illumina Multiplexing Sample Preparation Oligo-nucleotide Kit, and the HiSeq 2000 Paired-End Cluster Generation Kit according to the manufacturer’s instructions.

Article Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Article Snippet: Libraries were generated using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, CA, USA). .. The fragmented cDNA was treated with end-repair, A-tailing, adapter ligation and 10 cycles of PCR amplification.

Article Title: Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3)
Article Snippet: An RNA-Seq library was produced using the Illumina TruSeq stranded total RNA sample preparation kit in accordance with the manufacturer’s instruction (Illumina, San Diego, CA USA). .. Approximately 1 µg of total RNA was subjected to PCR amplification for cDNA synthesis, fragmentation, and adaptor ligation.

Article Title: Differential methylation of the TRPA1 promoter in pain sensitivity
Article Snippet: Samples were prepared for next-generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps. .. MeDIP DNA was then purified (Zymo Research) and amplified by 18 cycles adapter-mediated PCR.

Methylated DNA Immunoprecipitation Sequencing:

Article Title: Differential methylation of the TRPA1 promoter in pain sensitivity
Article Snippet: MeDIP sequencing MeDIP-seq was performed and analysed separately in the MZ twin and unrelated samples. .. Samples were prepared for next-generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps.

Electrophoresis:

Article Title: Transcription factor MrpC binds to promoter regions of hundreds of developmentally-regulated genes in Myxococcus xanthus
Article Snippet: DNA sequencing Samples of DNA (~10 ng) resulting from ChIP were processed using a ChIP-seq sample preparation kit according to the manufacturer’s instructions (Illumina). .. Each sample was size-selected by excising and extracting fragments of approximately 300 bp after electrophoresis on a 2% agarose gel, the DNA fragments were enriched by PCR, and the library was validated on an Agilent Technologies 2100 Bioanalyzer.

Expressing:

Article Title: CXCR2 Inhibition Combined with Sorafenib Improved Antitumor and Antiangiogenic Response in Preclinical Models of Ovarian Cancer
Article Snippet: .. Gene expression of ELR+ CXC chemokines Transcriptome sequencing was performed using the Illumina MiSeq sequencer and Illumina TruSeq RNA v2 sample preparation kit and protocols (Illumina, Inc.). ..

Article Title: Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Article Snippet: Libraries were produced using the Truseq RNA sample preparation kit from Illumina as described in the Materials and Methods. .. All the RNA-Seq data has been deposited in the Gene Expression Omnibus under the accession number GSE69822 .

Genome Wide:

Article Title: Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Article Snippet: Genome-wide mRNA profiling was performed by RNA-Seq on WT MCF10a cells starved overnight then stimulated with 10 ng/ml EGF for 15, 40, 90, 180 and 300 min (Figure ). .. Libraries were produced using the Truseq RNA sample preparation kit from Illumina as described in the Materials and Methods.

Flow Cytometry:

Article Title: Exome Sequencing Identifies a Missense Variant in EFEMP1 Co-Segregating in a Family with Autosomal Dominant Primary Open-Angle Glaucoma
Article Snippet: .. Captured DNA was eluted (NaOH) and then subject to flow-cell massively-parallel sequencing on a HiSeq2000 System (Illumina, San Diego, CA) using the Illumina Multiplexing Sample Preparation Oligo-nucleotide Kit, and the HiSeq 2000 Paired-End Cluster Generation Kit according to the manufacturer’s instructions. .. Briefly, hybrid-capture libraries were amplified to add indexing (identifying) tags and sequencing primers then subjected to paired-end (2 x 101 bp read length), multiplex sequencing-by-synthesis using fluorescent, cyclic reversible (3’-blocked) terminators.

Article Title: Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks
Article Snippet: TruSeq RNA sample preparation kit (Illumina) was used for paired‐end library construction according to the manufacturer's instructions. .. Each sample was barcoded with a unique sequence index tag, and pools of 12 different barcoded samples were loaded in 8 lanes of a single flow cell of Illumina HiScanSQ machine.

Ligation:

Article Title: High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli
Article Snippet: Illumina Deep Sequencing The sample preparation was performed using the Illumina DNA sample preparation kit, according to the manufacturer's instruction (New England Biolabs). .. Subsequently, adapters designed for library construction were ligated to the PCR fragments, ligation products were gel-purified to select for ∼180–300-bp fragments, and PCR amplification was performed to enrich for the ligated fragments.

Article Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Article Snippet: Libraries were generated using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, CA, USA). .. The fragmented cDNA was treated with end-repair, A-tailing, adapter ligation and 10 cycles of PCR amplification.

Article Title: Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3)
Article Snippet: An RNA-Seq library was produced using the Illumina TruSeq stranded total RNA sample preparation kit in accordance with the manufacturer’s instruction (Illumina, San Diego, CA USA). .. Approximately 1 µg of total RNA was subjected to PCR amplification for cDNA synthesis, fragmentation, and adaptor ligation.

Generated:

Article Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Article Snippet: .. Libraries were generated using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, CA, USA). .. Briefly, the rRNA-depleted RNA was fragmented and reversed transcribed using Superscript II (Invitrogen, Carlsbad, CA, USA), followed by second-strand synthesis.

DNA Sequencing:

Article Title: Transcription factor MrpC binds to promoter regions of hundreds of developmentally-regulated genes in Myxococcus xanthus
Article Snippet: .. DNA sequencing Samples of DNA (~10 ng) resulting from ChIP were processed using a ChIP-seq sample preparation kit according to the manufacturer’s instructions (Illumina). ..

Sequencing:

Article Title: High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli
Article Snippet: .. Illumina Deep Sequencing The sample preparation was performed using the Illumina DNA sample preparation kit, according to the manufacturer's instruction (New England Biolabs). ..

Article Title: CXCR2 Inhibition Combined with Sorafenib Improved Antitumor and Antiangiogenic Response in Preclinical Models of Ovarian Cancer
Article Snippet: .. Gene expression of ELR+ CXC chemokines Transcriptome sequencing was performed using the Illumina MiSeq sequencer and Illumina TruSeq RNA v2 sample preparation kit and protocols (Illumina, Inc.). ..

Article Title: Somatic mtDNA variation is an important component of Parkinson's disease
Article Snippet: .. 2.3 MtDNA sequencing Pooled amplicons were “tagmented,” amplified, cleaned, normalized, and pooled into 48 sample multiplexes using the Illumina Nextera XT DNA sample preparation kit (Illumina, CA, USA). .. Multiplex pools were sequenced using MiSeq Reagent Kit v3.0 (Illumina, CA, USA) in paired-end, 250 bp reads.

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: Paragraph title: Small RNA library preparation and sequencing ... Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively.

Article Title: Exome Sequencing Identifies a Missense Variant in EFEMP1 Co-Segregating in a Family with Autosomal Dominant Primary Open-Angle Glaucoma
Article Snippet: .. Captured DNA was eluted (NaOH) and then subject to flow-cell massively-parallel sequencing on a HiSeq2000 System (Illumina, San Diego, CA) using the Illumina Multiplexing Sample Preparation Oligo-nucleotide Kit, and the HiSeq 2000 Paired-End Cluster Generation Kit according to the manufacturer’s instructions. .. Briefly, hybrid-capture libraries were amplified to add indexing (identifying) tags and sequencing primers then subjected to paired-end (2 x 101 bp read length), multiplex sequencing-by-synthesis using fluorescent, cyclic reversible (3’-blocked) terminators.

Article Title: Transcription factor MrpC binds to promoter regions of hundreds of developmentally-regulated genes in Myxococcus xanthus
Article Snippet: DNA sequencing Samples of DNA (~10 ng) resulting from ChIP were processed using a ChIP-seq sample preparation kit according to the manufacturer’s instructions (Illumina). .. Sequencing was performed at the Michigan State University Research Support Technology Facility using a kit designed to produce reads of 36 nucleotides (Illumina) and a Solexa instrument.

Article Title: Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3)
Article Snippet: An RNA-Seq library was produced using the Illumina TruSeq stranded total RNA sample preparation kit in accordance with the manufacturer’s instruction (Illumina, San Diego, CA USA). .. Sequencing was performed on the NextSeq500 platform (Illumina).

Article Title: Differential methylation of the TRPA1 promoter in pain sensitivity
Article Snippet: Paragraph title: MeDIP sequencing ... Samples were prepared for next-generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps.

Article Title: Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Article Snippet: .. Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina). ..

Article Title: Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks
Article Snippet: Paragraph title: RNA library preparation and sequencing ... TruSeq RNA sample preparation kit (Illumina) was used for paired‐end library construction according to the manufacturer's instructions.

Sonication:

Article Title: Differential methylation of the TRPA1 promoter in pain sensitivity
Article Snippet: In the discovery MZ twin sample, 5 μg genomic DNA from each sample was sonicated on a Diagenode Bioruptor to produce a median fragment length of 180–230, and verified using a 2100 Bioanalyzer with DNA1000 chips (Agilent, Santa Clara, USA). .. Samples were prepared for next-generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps.

ChIP-sequencing:

Article Title: Transcription factor MrpC binds to promoter regions of hundreds of developmentally-regulated genes in Myxococcus xanthus
Article Snippet: .. DNA sequencing Samples of DNA (~10 ng) resulting from ChIP were processed using a ChIP-seq sample preparation kit according to the manufacturer’s instructions (Illumina). ..

Multiplexing:

Article Title: Exome Sequencing Identifies a Missense Variant in EFEMP1 Co-Segregating in a Family with Autosomal Dominant Primary Open-Angle Glaucoma
Article Snippet: .. Captured DNA was eluted (NaOH) and then subject to flow-cell massively-parallel sequencing on a HiSeq2000 System (Illumina, San Diego, CA) using the Illumina Multiplexing Sample Preparation Oligo-nucleotide Kit, and the HiSeq 2000 Paired-End Cluster Generation Kit according to the manufacturer’s instructions. .. Briefly, hybrid-capture libraries were amplified to add indexing (identifying) tags and sequencing primers then subjected to paired-end (2 x 101 bp read length), multiplex sequencing-by-synthesis using fluorescent, cyclic reversible (3’-blocked) terminators.

RNA Sequencing Assay:

Article Title: Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Article Snippet: Genome-wide mRNA profiling was performed by RNA-Seq on WT MCF10a cells starved overnight then stimulated with 10 ng/ml EGF for 15, 40, 90, 180 and 300 min (Figure ). .. Libraries were produced using the Truseq RNA sample preparation kit from Illumina as described in the Materials and Methods.

Article Title: Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3)
Article Snippet: .. An RNA-Seq library was produced using the Illumina TruSeq stranded total RNA sample preparation kit in accordance with the manufacturer’s instruction (Illumina, San Diego, CA USA). .. Approximately 1 µg of total RNA was subjected to PCR amplification for cDNA synthesis, fragmentation, and adaptor ligation.

Article Title: Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Article Snippet: Paragraph title: RNA-seq ... Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina).

Methylation:

Article Title: Differential methylation of the TRPA1 promoter in pain sensitivity
Article Snippet: Samples were prepared for next-generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps. .. One microgram of each adapter-ligated sample was spiked with ~5 × 10−7 pmoles methylated/unmethylated control DNA (see ref. for details) and subjected to MeDIP (ref. ) with 150 ng anti-5-methylcytidine using automation according to manufacturer’s reagents and protocols (Diagenode); 100 ng was reserved as input for MeDIP quality control (QC), which was conducted using quantitative PCR (qPCR) with primers designed to amplify methylated/unmethylated control DNA.

Isolation:

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: Firstly, the total RNA was isolated from gill tissues with TRIzol reagent (Invitrogen), and the RNA of 15–40 nt was purified by the 15% Polyacrylamide gel. .. Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively.

Article Title: Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3)
Article Snippet: Total RNA was isolated from non-treated control and PdNPs-treated SKOV3 cells. .. An RNA-Seq library was produced using the Illumina TruSeq stranded total RNA sample preparation kit in accordance with the manufacturer’s instruction (Illumina, San Diego, CA USA).

Article Title: Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Article Snippet: RNA-seq BMDM from LysM-Cre:NELF-B wt/wt (WT) and/or LysM-Cre:NELF-B fl/fl (NELF-B KO) mice were treated as indicated in individual figure legends (vehicle, LPS, LPS + Dex for 1 hr) and RNA was isolated using Qiagen RNA-easy kit. .. Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina).

Purification:

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: Firstly, the total RNA was isolated from gill tissues with TRIzol reagent (Invitrogen), and the RNA of 15–40 nt was purified by the 15% Polyacrylamide gel. .. Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively.

Article Title: Differential methylation of the TRPA1 promoter in pain sensitivity
Article Snippet: .. Samples were prepared for next-generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps. .. Samples were quantified and size checked using a 2100 Bioanalyzer and DNA1000 chips (Agilent).

Polymerase Chain Reaction:

Article Title: High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli
Article Snippet: Illumina Deep Sequencing The sample preparation was performed using the Illumina DNA sample preparation kit, according to the manufacturer's instruction (New England Biolabs). .. Subsequently, adapters designed for library construction were ligated to the PCR fragments, ligation products were gel-purified to select for ∼180–300-bp fragments, and PCR amplification was performed to enrich for the ligated fragments.

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively. .. The double-strand cDNA was performed followed by PCR amplification.

Article Title: Exome Sequencing Identifies a Missense Variant in EFEMP1 Co-Segregating in a Family with Autosomal Dominant Primary Open-Angle Glaucoma
Article Snippet: Briefly, genomic DNA (3 μg) was fragmented (150–200 bp) by acoustic shearing, ligated to adapter primers, and PCR-amplified. .. Captured DNA was eluted (NaOH) and then subject to flow-cell massively-parallel sequencing on a HiSeq2000 System (Illumina, San Diego, CA) using the Illumina Multiplexing Sample Preparation Oligo-nucleotide Kit, and the HiSeq 2000 Paired-End Cluster Generation Kit according to the manufacturer’s instructions.

Article Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Article Snippet: Libraries were generated using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, CA, USA). .. The fragmented cDNA was treated with end-repair, A-tailing, adapter ligation and 10 cycles of PCR amplification.

Article Title: Transcription factor MrpC binds to promoter regions of hundreds of developmentally-regulated genes in Myxococcus xanthus
Article Snippet: DNA sequencing Samples of DNA (~10 ng) resulting from ChIP were processed using a ChIP-seq sample preparation kit according to the manufacturer’s instructions (Illumina). .. Each sample was size-selected by excising and extracting fragments of approximately 300 bp after electrophoresis on a 2% agarose gel, the DNA fragments were enriched by PCR, and the library was validated on an Agilent Technologies 2100 Bioanalyzer.

Article Title: Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3)
Article Snippet: An RNA-Seq library was produced using the Illumina TruSeq stranded total RNA sample preparation kit in accordance with the manufacturer’s instruction (Illumina, San Diego, CA USA). .. Approximately 1 µg of total RNA was subjected to PCR amplification for cDNA synthesis, fragmentation, and adaptor ligation.

Article Title: Differential methylation of the TRPA1 promoter in pain sensitivity
Article Snippet: Samples were prepared for next-generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps. .. MeDIP DNA was then purified (Zymo Research) and amplified by 18 cycles adapter-mediated PCR.

cDNA Library Assay:

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: .. Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively. .. Then these small RNAs were ligated sequentially to 5′ and 3′ adapters and used SuperScript II Reverse Transcriptase (Life Technologies) to synthesize the first-strand cDNA.

Sample Prep:

Article Title: High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli
Article Snippet: .. Illumina Deep Sequencing The sample preparation was performed using the Illumina DNA sample preparation kit, according to the manufacturer's instruction (New England Biolabs). ..

Article Title: CXCR2 Inhibition Combined with Sorafenib Improved Antitumor and Antiangiogenic Response in Preclinical Models of Ovarian Cancer
Article Snippet: .. Gene expression of ELR+ CXC chemokines Transcriptome sequencing was performed using the Illumina MiSeq sequencer and Illumina TruSeq RNA v2 sample preparation kit and protocols (Illumina, Inc.). ..

Article Title: Somatic mtDNA variation is an important component of Parkinson's disease
Article Snippet: .. 2.3 MtDNA sequencing Pooled amplicons were “tagmented,” amplified, cleaned, normalized, and pooled into 48 sample multiplexes using the Illumina Nextera XT DNA sample preparation kit (Illumina, CA, USA). .. Multiplex pools were sequenced using MiSeq Reagent Kit v3.0 (Illumina, CA, USA) in paired-end, 250 bp reads.

Article Title: High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response
Article Snippet: .. Equal amounts of the high-quality small RNA samples from six individuals of each group were then pooled for cDNA library preparation using the TruSeq Small RNA sample Preparation Kit (Illumina), respectively. .. Then these small RNAs were ligated sequentially to 5′ and 3′ adapters and used SuperScript II Reverse Transcriptase (Life Technologies) to synthesize the first-strand cDNA.

Article Title: Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Article Snippet: .. Libraries were produced using the Truseq RNA sample preparation kit from Illumina as described in the Materials and Methods. .. All the RNA-Seq data has been deposited in the Gene Expression Omnibus under the accession number GSE69822 .

Article Title: Exome Sequencing Identifies a Missense Variant in EFEMP1 Co-Segregating in a Family with Autosomal Dominant Primary Open-Angle Glaucoma
Article Snippet: .. Captured DNA was eluted (NaOH) and then subject to flow-cell massively-parallel sequencing on a HiSeq2000 System (Illumina, San Diego, CA) using the Illumina Multiplexing Sample Preparation Oligo-nucleotide Kit, and the HiSeq 2000 Paired-End Cluster Generation Kit according to the manufacturer’s instructions. .. Briefly, hybrid-capture libraries were amplified to add indexing (identifying) tags and sequencing primers then subjected to paired-end (2 x 101 bp read length), multiplex sequencing-by-synthesis using fluorescent, cyclic reversible (3’-blocked) terminators.

Article Title: Metatranscriptomic insights on gene expression and regulatory controls in Candidatus Accumulibacter phosphatis
Article Snippet: .. Libraries were generated using the Truseq Stranded mRNA sample preparation kit (Illumina, San Diego, CA, USA). .. Briefly, the rRNA-depleted RNA was fragmented and reversed transcribed using Superscript II (Invitrogen, Carlsbad, CA, USA), followed by second-strand synthesis.

Article Title: Transcription factor MrpC binds to promoter regions of hundreds of developmentally-regulated genes in Myxococcus xanthus
Article Snippet: .. DNA sequencing Samples of DNA (~10 ng) resulting from ChIP were processed using a ChIP-seq sample preparation kit according to the manufacturer’s instructions (Illumina). ..

Article Title: Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3)
Article Snippet: .. An RNA-Seq library was produced using the Illumina TruSeq stranded total RNA sample preparation kit in accordance with the manufacturer’s instruction (Illumina, San Diego, CA USA). .. Approximately 1 µg of total RNA was subjected to PCR amplification for cDNA synthesis, fragmentation, and adaptor ligation.

Article Title: Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Article Snippet: .. Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina). ..

Article Title: Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks
Article Snippet: .. TruSeq RNA sample preparation kit (Illumina) was used for paired‐end library construction according to the manufacturer's instructions. .. Each sample was barcoded with a unique sequence index tag, and pools of 12 different barcoded samples were loaded in 8 lanes of a single flow cell of Illumina HiScanSQ machine.

Mouse Assay:

Article Title: Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages
Article Snippet: RNA-seq BMDM from LysM-Cre:NELF-B wt/wt (WT) and/or LysM-Cre:NELF-B fl/fl (NELF-B KO) mice were treated as indicated in individual figure legends (vehicle, LPS, LPS + Dex for 1 hr) and RNA was isolated using Qiagen RNA-easy kit. .. Total RNA was polyA enriched and converted into Illumina-compatible sequencing library with TruSeq mRNA-Seq sample preparation kit (Illumina).

Chromatin Immunoprecipitation:

Article Title: Transcription factor MrpC binds to promoter regions of hundreds of developmentally-regulated genes in Myxococcus xanthus
Article Snippet: .. DNA sequencing Samples of DNA (~10 ng) resulting from ChIP were processed using a ChIP-seq sample preparation kit according to the manufacturer’s instructions (Illumina). ..

Article Title: Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3)
Article Snippet: The quantity and quality of the RNA were determined using a Bioanalyzer RNA chip (Agilent, Santa Clara, CA, USA). .. An RNA-Seq library was produced using the Illumina TruSeq stranded total RNA sample preparation kit in accordance with the manufacturer’s instruction (Illumina, San Diego, CA USA).

Real-time Polymerase Chain Reaction:

Article Title: Differential methylation of the TRPA1 promoter in pain sensitivity
Article Snippet: Samples were prepared for next-generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps. .. One microgram of each adapter-ligated sample was spiked with ~5 × 10−7 pmoles methylated/unmethylated control DNA (see ref. for details) and subjected to MeDIP (ref. ) with 150 ng anti-5-methylcytidine using automation according to manufacturer’s reagents and protocols (Diagenode); 100 ng was reserved as input for MeDIP quality control (QC), which was conducted using quantitative PCR (qPCR) with primers designed to amplify methylated/unmethylated control DNA.

Multiplex Assay:

Article Title: Somatic mtDNA variation is an important component of Parkinson's disease
Article Snippet: 2.3 MtDNA sequencing Pooled amplicons were “tagmented,” amplified, cleaned, normalized, and pooled into 48 sample multiplexes using the Illumina Nextera XT DNA sample preparation kit (Illumina, CA, USA). .. Multiplex pools were sequenced using MiSeq Reagent Kit v3.0 (Illumina, CA, USA) in paired-end, 250 bp reads.

Article Title: Exome Sequencing Identifies a Missense Variant in EFEMP1 Co-Segregating in a Family with Autosomal Dominant Primary Open-Angle Glaucoma
Article Snippet: Captured DNA was eluted (NaOH) and then subject to flow-cell massively-parallel sequencing on a HiSeq2000 System (Illumina, San Diego, CA) using the Illumina Multiplexing Sample Preparation Oligo-nucleotide Kit, and the HiSeq 2000 Paired-End Cluster Generation Kit according to the manufacturer’s instructions. .. Briefly, hybrid-capture libraries were amplified to add indexing (identifying) tags and sequencing primers then subjected to paired-end (2 x 101 bp read length), multiplex sequencing-by-synthesis using fluorescent, cyclic reversible (3’-blocked) terminators.

Selection:

Article Title: Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3)
Article Snippet: An RNA-Seq library was produced using the Illumina TruSeq stranded total RNA sample preparation kit in accordance with the manufacturer’s instruction (Illumina, San Diego, CA USA). .. After size selection according to agarose gels, a second PCR amplification was carried out.

Agarose Gel Electrophoresis:

Article Title: Transcription factor MrpC binds to promoter regions of hundreds of developmentally-regulated genes in Myxococcus xanthus
Article Snippet: DNA sequencing Samples of DNA (~10 ng) resulting from ChIP were processed using a ChIP-seq sample preparation kit according to the manufacturer’s instructions (Illumina). .. Each sample was size-selected by excising and extracting fragments of approximately 300 bp after electrophoresis on a 2% agarose gel, the DNA fragments were enriched by PCR, and the library was validated on an Agilent Technologies 2100 Bioanalyzer.

Next-Generation Sequencing:

Article Title: Differential methylation of the TRPA1 promoter in pain sensitivity
Article Snippet: .. Samples were prepared for next-generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps. .. Samples were quantified and size checked using a 2100 Bioanalyzer and DNA1000 chips (Agilent).

Produced:

Article Title: Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop
Article Snippet: .. Libraries were produced using the Truseq RNA sample preparation kit from Illumina as described in the Materials and Methods. .. All the RNA-Seq data has been deposited in the Gene Expression Omnibus under the accession number GSE69822 .

Article Title: Cytotoxicity and Transcriptomic Analyses of Biogenic Palladium Nanoparticles in Human Ovarian Cancer Cells (SKOV3)
Article Snippet: .. An RNA-Seq library was produced using the Illumina TruSeq stranded total RNA sample preparation kit in accordance with the manufacturer’s instruction (Illumina, San Diego, CA USA). .. Approximately 1 µg of total RNA was subjected to PCR amplification for cDNA synthesis, fragmentation, and adaptor ligation.

Concentration Assay:

Article Title: Transcriptome profiling of immune tissues reveals habitat‐specific gene expression between lake and river sticklebacks
Article Snippet: RNA was quantified with NanoDrop and Bioanalyzer, and ~1 μg of RNA in a concentration of 20 ng/μL was used for library construction. .. TruSeq RNA sample preparation kit (Illumina) was used for paired‐end library construction according to the manufacturer's instructions.

Methylated DNA Immunoprecipitation:

Article Title: Differential methylation of the TRPA1 promoter in pain sensitivity
Article Snippet: Paragraph title: MeDIP sequencing ... Samples were prepared for next-generation sequencing by blunt ending, dA-tailing and then ligating paired-end adapters according to manufacturer’s reagents and protocols (Illumina) with purification (QIAGEN) between steps.

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    Comparison or mRNA-seq libraries from <t>oligo-dT</t> and Cap-captured mRNA. A-B. Reads from dT or Cap-capture prepared libraries were aligned to sequences consisting of the 5’ or 3’ 25% of Refseq <t>mRNAs.</t> Reads aligning to the 5’ and 3’ portions of the transcript are plotted. Blue line indicates a ratio of one. C. Reads from mRNA-seq libraries prepared using oligo-dT captured mRNAs from mitotic and interphase Xenopus egg extract were aligned to the Xenopus laevis Unigene database. Relative abundance of each mRNA in mitotic and interphase extracts is plotted. Red points highlight two-fold differences between mitotic and interphase samples. D. Same experiment as in panel C except that the mRNAs were purified using Cap-capture prior to library preparation. Red points highlight two-fold differences. E. Scatterplot of mRNA abundance in oligo-dT-captured and Cap-captured mRNA libraries. F. The ratio of reads per mRNA in mitotic and interphase extracts are plotted for oligo-dT captured mRNAs (X-axis, data from panel A) and cap-captured mRNAs (Y-axis data from panel B). The colored points correspond to mRNAs with known changes in poly-A tail length (cdk1, green; Eg2/aurora-a, orange; mos, red; Xlcl1, yellow). Quadrants highlight two-fold differences between samples.
    Oligo Dt, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc illumina oligo
    Quantification of synthetic double-stranded oligos. Four dilutions of two synthetic double-stranded oligos consisting of either the Ion Torrent “A” and “P1” adapter sequences ( a ) or the <t>Illumina</t> “i7” and “i5” adapter sequences ( b ) were quantified in duplicate with the NanoDrop ( ), Qubit ( ), Bioanalyzer ( ), GX Touch ( ), TapeStation ( ), and Fragment Analyzer ( ). The mean of the measured <t>oligo</t> concentrations were plotted against the concentrations given by the oligo supplier.
    Illumina Oligo, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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
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    Comparison or mRNA-seq libraries from oligo-dT and Cap-captured mRNA. A-B. Reads from dT or Cap-capture prepared libraries were aligned to sequences consisting of the 5’ or 3’ 25% of Refseq mRNAs. Reads aligning to the 5’ and 3’ portions of the transcript are plotted. Blue line indicates a ratio of one. C. Reads from mRNA-seq libraries prepared using oligo-dT captured mRNAs from mitotic and interphase Xenopus egg extract were aligned to the Xenopus laevis Unigene database. Relative abundance of each mRNA in mitotic and interphase extracts is plotted. Red points highlight two-fold differences between mitotic and interphase samples. D. Same experiment as in panel C except that the mRNAs were purified using Cap-capture prior to library preparation. Red points highlight two-fold differences. E. Scatterplot of mRNA abundance in oligo-dT-captured and Cap-captured mRNA libraries. F. The ratio of reads per mRNA in mitotic and interphase extracts are plotted for oligo-dT captured mRNAs (X-axis, data from panel A) and cap-captured mRNAs (Y-axis data from panel B). The colored points correspond to mRNAs with known changes in poly-A tail length (cdk1, green; Eg2/aurora-a, orange; mos, red; Xlcl1, yellow). Quadrants highlight two-fold differences between samples.

    Journal: PLoS ONE

    Article Title: Combining Different mRNA Capture Methods to Analyze the Transcriptome: Analysis of the Xenopus laevis Transcriptome

    doi: 10.1371/journal.pone.0077700

    Figure Lengend Snippet: Comparison or mRNA-seq libraries from oligo-dT and Cap-captured mRNA. A-B. Reads from dT or Cap-capture prepared libraries were aligned to sequences consisting of the 5’ or 3’ 25% of Refseq mRNAs. Reads aligning to the 5’ and 3’ portions of the transcript are plotted. Blue line indicates a ratio of one. C. Reads from mRNA-seq libraries prepared using oligo-dT captured mRNAs from mitotic and interphase Xenopus egg extract were aligned to the Xenopus laevis Unigene database. Relative abundance of each mRNA in mitotic and interphase extracts is plotted. Red points highlight two-fold differences between mitotic and interphase samples. D. Same experiment as in panel C except that the mRNAs were purified using Cap-capture prior to library preparation. Red points highlight two-fold differences. E. Scatterplot of mRNA abundance in oligo-dT-captured and Cap-captured mRNA libraries. F. The ratio of reads per mRNA in mitotic and interphase extracts are plotted for oligo-dT captured mRNAs (X-axis, data from panel A) and cap-captured mRNAs (Y-axis data from panel B). The colored points correspond to mRNAs with known changes in poly-A tail length (cdk1, green; Eg2/aurora-a, orange; mos, red; Xlcl1, yellow). Quadrants highlight two-fold differences between samples.

    Article Snippet: To compare the mRNAs sampled by oligo-dT and Cap-capture methods we prepared Illumina libraries from Xenopus laevis egg extracts arrested in metaphase of meiosis II (labeled Mitosis or M for the remainder of the paper) and extracts induced to enter interphase (IF) by the addition of calcium, which mimics fertilization induced calcium release[ ].

    Techniques: Purification

    Poly-A tail analysis of selected mRNAs. mRNAs that exhibited changes in Mitosis:Interphase (M:IF) abundance ratios in oligo-dT-captured samples, but not in Cap-captured samples were analyzed for poly-A tail length using the ePAT assay and anchored TVN reverse transcription controls. A. Six mRNAs with high M:IF ratios (aurora-a, esco2, fbox5, stx11, march7, and hexim1) showed longer poly-A tails in mitotic extract. Two mRNA (setd8 and MGC83922) with a low M:IF ratio showed very modest changes in poly-A tail lengths between Mitosis and Interphase. Red asterix indicates the position of the prominent TVN PCR product that is quantified in B. B. The amount of PCR product contained in the TVN-RT PCR reactions (red asterix in A) were quantified. The ratio of the amount of PCR product in Mitotic to Interphase extracts is presented in the first line. The ratio of each mRNA in Mitotic and Interphase extracts as determined by RNA-seq is presented below the PCR derived ratios for comparison. In addition five mRNAs with high M:IF ratios (aurora-1, fbox5, stx11, march7, and hexim1) had increased amounts of minimal poly-A tail PCR products in mitosis compared to interphase in TVN controls (quantified below gel) while both setd8 and MGC88922 had higher levels of TVN PCR products in interphase compared to mitotic extracts TVN PCR products indicate mRNAs with poly-A tails of 18 As. Line traces of ePAT PCR reactions presented in panel A. Black lines indicate traces from mitotic extract and red lines indicate traces from interaphse extract. D. Semi-quantitative PCR for each of the mRNAs tested in A was performed on RNA from mitotic and interphase extracts. Random hexamers were used to prime reverse transcription for these reactions. A second experiment showing very similar results is present in Figure S2.

    Journal: PLoS ONE

    Article Title: Combining Different mRNA Capture Methods to Analyze the Transcriptome: Analysis of the Xenopus laevis Transcriptome

    doi: 10.1371/journal.pone.0077700

    Figure Lengend Snippet: Poly-A tail analysis of selected mRNAs. mRNAs that exhibited changes in Mitosis:Interphase (M:IF) abundance ratios in oligo-dT-captured samples, but not in Cap-captured samples were analyzed for poly-A tail length using the ePAT assay and anchored TVN reverse transcription controls. A. Six mRNAs with high M:IF ratios (aurora-a, esco2, fbox5, stx11, march7, and hexim1) showed longer poly-A tails in mitotic extract. Two mRNA (setd8 and MGC83922) with a low M:IF ratio showed very modest changes in poly-A tail lengths between Mitosis and Interphase. Red asterix indicates the position of the prominent TVN PCR product that is quantified in B. B. The amount of PCR product contained in the TVN-RT PCR reactions (red asterix in A) were quantified. The ratio of the amount of PCR product in Mitotic to Interphase extracts is presented in the first line. The ratio of each mRNA in Mitotic and Interphase extracts as determined by RNA-seq is presented below the PCR derived ratios for comparison. In addition five mRNAs with high M:IF ratios (aurora-1, fbox5, stx11, march7, and hexim1) had increased amounts of minimal poly-A tail PCR products in mitosis compared to interphase in TVN controls (quantified below gel) while both setd8 and MGC88922 had higher levels of TVN PCR products in interphase compared to mitotic extracts TVN PCR products indicate mRNAs with poly-A tails of 18 As. Line traces of ePAT PCR reactions presented in panel A. Black lines indicate traces from mitotic extract and red lines indicate traces from interaphse extract. D. Semi-quantitative PCR for each of the mRNAs tested in A was performed on RNA from mitotic and interphase extracts. Random hexamers were used to prime reverse transcription for these reactions. A second experiment showing very similar results is present in Figure S2.

    Article Snippet: To compare the mRNAs sampled by oligo-dT and Cap-capture methods we prepared Illumina libraries from Xenopus laevis egg extracts arrested in metaphase of meiosis II (labeled Mitosis or M for the remainder of the paper) and extracts induced to enter interphase (IF) by the addition of calcium, which mimics fertilization induced calcium release[ ].

    Techniques: Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, RNA Sequencing Assay, Derivative Assay, Real-time Polymerase Chain Reaction

    Quantification of synthetic double-stranded oligos. Four dilutions of two synthetic double-stranded oligos consisting of either the Ion Torrent “A” and “P1” adapter sequences ( a ) or the Illumina “i7” and “i5” adapter sequences ( b ) were quantified in duplicate with the NanoDrop ( ), Qubit ( ), Bioanalyzer ( ), GX Touch ( ), TapeStation ( ), and Fragment Analyzer ( ). The mean of the measured oligo concentrations were plotted against the concentrations given by the oligo supplier.

    Journal: Scientific Reports

    Article Title: Quantification of massively parallel sequencing libraries – a comparative study of eight methods

    doi: 10.1038/s41598-018-19574-w

    Figure Lengend Snippet: Quantification of synthetic double-stranded oligos. Four dilutions of two synthetic double-stranded oligos consisting of either the Ion Torrent “A” and “P1” adapter sequences ( a ) or the Illumina “i7” and “i5” adapter sequences ( b ) were quantified in duplicate with the NanoDrop ( ), Qubit ( ), Bioanalyzer ( ), GX Touch ( ), TapeStation ( ), and Fragment Analyzer ( ). The mean of the measured oligo concentrations were plotted against the concentrations given by the oligo supplier.

    Article Snippet: The Illumina oligo was identical to the “i7” and “i5” adapter sequences.

    Techniques:

    Intragenic copy number detection and comparison to commercial panels. ( A ) Control genomic DNA samples were acquired from kConFab for sensitivity testing. Three of these samples included known exon duplications in BRCA1 , TP53 and MSH2 , which were assessed by the DeCON tool. Exons are numbered along the x-axis, and those of normal copy number are presented as blue dots. Amplifications are shown in red. The TP53 and AURKB genes are on opposing DNA strands hence the presence of the latter and its exons in this Figure. A similar genetic-overlap is observed for MSH2 to the left of the panel. ( B ) A commercially available pool of synthetic oligos against a normal genomic background was also obtained. Mutations were provided at variant allele frequencies (VAF) of 5–15% and 15–35%, or at germline frequencies. Presented are the number of detected and missed variants in our PV1 and PV2 panels relative to what was expected in AcroMetrix. This was compared to three other panels [AmpliSeq Cancer Hotspot Panel v2 (CHPv2), Illumina TruSeq Amplicon – Cancer Panel (TSCAP) and TruSight Tumor Panel 26 (TSTP)], the data for which were provided by the AcroMetrix manufacturer. Percent values on the right indicate the proportion of AcroMetrix variants actually targeted by the panels.

    Journal: Scientific Reports

    Article Title: Development and validation of a targeted gene sequencing panel for application to disparate cancers

    doi: 10.1038/s41598-019-52000-3

    Figure Lengend Snippet: Intragenic copy number detection and comparison to commercial panels. ( A ) Control genomic DNA samples were acquired from kConFab for sensitivity testing. Three of these samples included known exon duplications in BRCA1 , TP53 and MSH2 , which were assessed by the DeCON tool. Exons are numbered along the x-axis, and those of normal copy number are presented as blue dots. Amplifications are shown in red. The TP53 and AURKB genes are on opposing DNA strands hence the presence of the latter and its exons in this Figure. A similar genetic-overlap is observed for MSH2 to the left of the panel. ( B ) A commercially available pool of synthetic oligos against a normal genomic background was also obtained. Mutations were provided at variant allele frequencies (VAF) of 5–15% and 15–35%, or at germline frequencies. Presented are the number of detected and missed variants in our PV1 and PV2 panels relative to what was expected in AcroMetrix. This was compared to three other panels [AmpliSeq Cancer Hotspot Panel v2 (CHPv2), Illumina TruSeq Amplicon – Cancer Panel (TSCAP) and TruSight Tumor Panel 26 (TSTP)], the data for which were provided by the AcroMetrix manufacturer. Percent values on the right indicate the proportion of AcroMetrix variants actually targeted by the panels.

    Article Snippet: Oligos were captured with PV1 and sequenced on Illumina’s NextSeq500 platform in multiplexed pools.

    Techniques: Variant Assay, Amplification

    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