Structured Review

Agilent technologies qubit fluorometer
Qubit Fluorometer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 92 stars, based on 30 article reviews
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qubit fluorometer - by Bioz Stars, 2019-10
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Amplification:

Article Title: Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development
Article Snippet: Amplified libraries were purified twice with Agencourt Ampure XP beads (Beckman Coulter, Cat#A63880) with a bead-to-sample ratio of 1.8:1. .. A Qubit fluorometer and Aglient Bioanalyzer were used to check library quality and concentration.

Article Title: Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling
Article Snippet: Paragraph title: RNA Amplification and Library Preparation ... Prior to sequencing, libraries were evaluated by Qubit fluorometer and TapeStation (Agilent).

Article Title: Nuclear Transcriptomes at High Resolution Using Retooled INTACT
Article Snippet: T-DNA enriched DNA and was amplified by 14 cycles of PCR using primers P5 and P7. .. The quality of the final multiplexed libraries was assessed by use of the Qubit fluorometer and an Agilent Bioanalyzer DNA 1000 assay.

Article Title: Consumption of Goats’ Milk Protects Mice From Carbon Tetrachloride-Induced Acute Hepatic Injury and Improves the Associated Gut Microbiota Imbalance
Article Snippet: The V3–V4 regions of the 16S rRNA gene were amplified using specific primers (forward primer 338F and reverse primer 806R; Table ) ( ). .. The DNA library was quantified using a Qubit Fluorometer and an Agilent Bioanalyzer 2100; sequencing was done using an Illumina HiSeq 2500 System.

Article Title: Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period
Article Snippet: To assess possible reagent contamination, each PCR reaction included a no template control (NTC) sample. .. The PCR product was purified and concentration and quality were determined for each amplicon using Qubit™ fluorometer and Agilent Bioanalyzer 2100. .. Barcoded amplicons were sequenced on an Ion Torrent Personal Genome Machine (PGM) with the Ion 318 Chip Kit v2 (Life Technologies) and the Ion PGM™ Sequencing 400 Kit (Life Technologies) under manufacturer’s conditions.

Article Title: Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India
Article Snippet: 1 ng of Qubit-quantified genomic DNA was tagmented (fragmented and tagged) using Amplicon Tagment Mix provided in the Nextera XT Kit. .. Quantification and size distribution of the prepared libraries were determined using Qubit fluorometer and the Agilent D1000 TapeStation respectively according to the manufacturer’s instructions.

Article Title: Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq
Article Snippet: All oligos were purchased from Integrated DNA Technologies with Standard Desalting. .. DNA fragments between 175 and 450 bp amplicon libraries were excised from the agarose gel and quantified by Qubit Fluorometer, Agilent 2100 Bioanalyzer and qRT-PCR. .. Excised libraries were then pooled, loaded onto two flow cell lanes and sequenced on the Hiseq2500 platform.

Synthesized:

Article Title: Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Article Snippet: Libraries were synthesized using Illumina TruSeq Stranded mRNA sample preparation kit from 500 ng of purified total RNA and indexed adapters according to the manufacturer’s protocol (Illumina). .. The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

Quantitative RT-PCR:

Article Title: Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Article Snippet: Libraries were synthesized using Illumina TruSeq Stranded mRNA sample preparation kit from 500 ng of purified total RNA and indexed adapters according to the manufacturer’s protocol (Illumina). .. The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. .. Pooled libraries were subjected to 35-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NextSeq 500).

Article Title: A minimal RNA ligand for potent RIG-I activation in living mice
Article Snippet: Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. .. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent 2200 TapeStation, and qRT-PCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols. .. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 500 sequencer with paired-end 75-bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

Article Title: Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq
Article Snippet: All oligos were purchased from Integrated DNA Technologies with Standard Desalting. .. DNA fragments between 175 and 450 bp amplicon libraries were excised from the agarose gel and quantified by Qubit Fluorometer, Agilent 2100 Bioanalyzer and qRT-PCR. .. Excised libraries were then pooled, loaded onto two flow cell lanes and sequenced on the Hiseq2500 platform.

Electrophoresis:

Article Title: A Systematic Analysis on mRNA and MicroRNA Expression in Runting and Stunting Chickens
Article Snippet: Total RNA was extracted from 5 RSS and 5 normal chicken livers using Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. .. Total RNA was tested via agarose electrophoresis, Qubit-fluorometer and Agilent 2100. .. The five RNA samples isolated from each type of chicken were pooled with equal amounts from individual chickens.

Incubation:

Article Title: Nuclear Transcriptomes at High Resolution Using Retooled INTACT
Article Snippet: After bead capture, DNA was eluted by incubation for 10 min in 50 µL 125 n m NaOH, diluted with 50 µL Tris-HCl (pH 8.8) and purified using AMPure XP beads. .. The quality of the final multiplexed libraries was assessed by use of the Qubit fluorometer and an Agilent Bioanalyzer DNA 1000 assay.

Article Title: Gene expression plasticity across hosts of an invasive scale insect species
Article Snippet: RNA yields and qualities were assessed using a Qubit fluorometer and an Agilent 2100 Bioanalyzer at the Denmark Technical University Multi-Assay Core (DMAC). .. RNA yields and qualities were assessed using a Qubit fluorometer and an Agilent 2100 Bioanalyzer at the Denmark Technical University Multi-Assay Core (DMAC).

Article Title: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
Article Snippet: Following washes, samples were eluted with Elution Buffer (1% SDS, 0.1M NaHCO3 ) and incubated at room temperature for 15 min. Elution reactions were pooled and incubated with NaCl overnight at 65°C to reverse crosslinks. .. Libraries were checked with Qubit fluorometer and Bioanalyzer (Agilent) assays and sequenced on the Illumina NextSeq 500 platform to generate single-end 75-bp reads.

Expressing:

Article Title: Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling
Article Snippet: We used a derivation of MARS-seq as described , to produce expression libraries with a minimum of three replicates per population. .. Prior to sequencing, libraries were evaluated by Qubit fluorometer and TapeStation (Agilent).

Article Title: H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression
Article Snippet: The resultant dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and quantitative reverse transcription PCR using the Kapa Biosystems Library Quantification Kit according to the manufacturer’s protocols. .. The resultant dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and quantitative reverse transcription PCR using the Kapa Biosystems Library Quantification Kit according to the manufacturer’s protocols.

Article Title: Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Article Snippet: The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. .. The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

Modification:

Article Title: Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq
Article Snippet: For selective SB insertion site sequencing by HiSeq (Illumina), we modified a published splinkerette PCR protocol . gDNA (3 µg per sample) was acoustically sheared to 200 bp using Covaris S220 Focused-ultrasonicator and end repaired using Fast DNA End Repair Kit (Thermo Fisher Scientific). .. DNA fragments between 175 and 450 bp amplicon libraries were excised from the agarose gel and quantified by Qubit Fluorometer, Agilent 2100 Bioanalyzer and qRT-PCR.

Chloramphenicol Acetyltransferase Assay:

Article Title: Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development
Article Snippet: Amplified libraries were purified twice with Agencourt Ampure XP beads (Beckman Coulter, CatA63880) with a bead-to-sample ratio of 1.8:1. .. A Qubit fluorometer and Aglient Bioanalyzer were used to check library quality and concentration.

Derivative Assay:

Article Title: Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Article Snippet: Total RNA was isolated from BMDMs derived from WT, Arhgef2 −/− , and Irf5 −/− mice, using RNeasy Micro kit (Qiagen). .. The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

Article Title: Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period
Article Snippet: Briefly, each of the primers contained a unique barcode, so that the derived sequences can be sorted into the respective sample bioinformatically in downstream analysis. .. The PCR product was purified and concentration and quality were determined for each amplicon using Qubit™ fluorometer and Agilent Bioanalyzer 2100.

Hybridization:

Article Title: Nuclear Transcriptomes at High Resolution Using Retooled INTACT
Article Snippet: The hybridization mix was incubated at 62°C for 48 h. DNA hybrids were captured for 30 min at room temperature using Streptavidin MyOne C1 Dynabeads (Life Technologies). .. The quality of the final multiplexed libraries was assessed by use of the Qubit fluorometer and an Agilent Bioanalyzer DNA 1000 assay.

Flow Cytometry:

Article Title: Treatment of Human Glioblastoma with a Live Attenuated Zika Virus Vaccine Candidate
Article Snippet: The quantities and qualities of the libraries were also assessed by the use of the Qubit Fluorometer and Agilent 2100 Bioanalyzer, respectively, and their molar concentrations were validated by qPCR for library pooling. .. The quantities and qualities of the libraries were also assessed by the use of the Qubit Fluorometer and Agilent 2100 Bioanalyzer, respectively, and their molar concentrations were validated by qPCR for library pooling.

Article Title: Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India
Article Snippet: Library preparation was performed at Genotypic Technology’s Genomics facility following Nextera XT DNA Library Preparation protocol (Cat #FC-131-1024). .. Quantification and size distribution of the prepared libraries were determined using Qubit fluorometer and the Agilent D1000 TapeStation respectively according to the manufacturer’s instructions.

Article Title: Gene expression plasticity across hosts of an invasive scale insect species
Article Snippet: RNA yields and qualities were assessed using a Qubit fluorometer and an Agilent 2100 Bioanalyzer at the Denmark Technical University Multi-Assay Core (DMAC). .. RNA yields and qualities were assessed using a Qubit fluorometer and an Agilent 2100 Bioanalyzer at the Denmark Technical University Multi-Assay Core (DMAC).

Ligation:

Article Title: Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling
Article Snippet: The resulting RNA was fragmented and converted into an Illumina sequencing-ready library through ligation, RT, and PCR. .. Prior to sequencing, libraries were evaluated by Qubit fluorometer and TapeStation (Agilent).

Infection:

Article Title: Treatment of Human Glioblastoma with a Live Attenuated Zika Virus Vaccine Candidate
Article Snippet: GSCs were infected with ZIKV at an MOI of 1, and total cellular RNA was extracted at 48 h postinfection with a PureLink RNA minikit (Life Technologies). .. The quantities and qualities of the libraries were also assessed by the use of the Qubit Fluorometer and Agilent 2100 Bioanalyzer, respectively, and their molar concentrations were validated by qPCR for library pooling.

Polymerase Chain Reaction:

Article Title: Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development
Article Snippet: After tagmentation, transposed DNA fragments were amplified using the following PCR condition (1 cycle of 72 °C for 5 min and 98 °C for 30 s, followed by 12 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min). .. A Qubit fluorometer and Aglient Bioanalyzer were used to check library quality and concentration.

Article Title: Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling
Article Snippet: The resulting RNA was fragmented and converted into an Illumina sequencing-ready library through ligation, RT, and PCR. .. Prior to sequencing, libraries were evaluated by Qubit fluorometer and TapeStation (Agilent).

Article Title: Nuclear Transcriptomes at High Resolution Using Retooled INTACT
Article Snippet: T-DNA enriched DNA and was amplified by 14 cycles of PCR using primers P5 and P7. .. The quality of the final multiplexed libraries was assessed by use of the Qubit fluorometer and an Agilent Bioanalyzer DNA 1000 assay.

Article Title: H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression
Article Snippet: RNA libraries were prepared using Illumina TruSeq Stranded mRNA Sample Preparation Kits from 500 ng of purified total RNA according to the manufacturer’s protocol. .. The resultant dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and quantitative reverse transcription PCR using the Kapa Biosystems Library Quantification Kit according to the manufacturer’s protocols. .. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on a single Illumina NextSeq500 run with single-end 75 bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

Article Title: Consumption of Goats’ Milk Protects Mice From Carbon Tetrachloride-Induced Acute Hepatic Injury and Improves the Associated Gut Microbiota Imbalance
Article Snippet: A TruSeq® DNA PCR-Free Sample Preparation Kit was used to construct the DNA library. .. The DNA library was quantified using a Qubit Fluorometer and an Agilent Bioanalyzer 2100; sequencing was done using an Illumina HiSeq 2500 System.

Article Title: Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period
Article Snippet: To assess possible reagent contamination, each PCR reaction included a no template control (NTC) sample. .. The PCR product was purified and concentration and quality were determined for each amplicon using Qubit™ fluorometer and Agilent Bioanalyzer 2100. .. Barcoded amplicons were sequenced on an Ion Torrent Personal Genome Machine (PGM) with the Ion 318 Chip Kit v2 (Life Technologies) and the Ion PGM™ Sequencing 400 Kit (Life Technologies) under manufacturer’s conditions.

Article Title: Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India
Article Snippet: The PCR product was purified using HighPrep beads (Magbio Genomics, #AC-60050). .. Quantification and size distribution of the prepared libraries were determined using Qubit fluorometer and the Agilent D1000 TapeStation respectively according to the manufacturer’s instructions.

Article Title: Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq
Article Snippet: Nested secondary PCR was performed using indexed SB-2ndR primer (5′- CAA GCA GAA GAC GGC ATA CGA GAT (8 bp index) GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC TTA GGG CTC CGC TTA AGG GAC-3′), SB-RF primer (AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T (1–4 bp stagger) GGC TAA GGT GTA TGT AAA CTT CCG ACT TCA ACT G-3′), and SB-LF primer (AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T (1–4 bp stagger) AAC TTA AGT GTA TGT AAA CTT CCG ACT TCA ACT G-3′). .. DNA fragments between 175 and 450 bp amplicon libraries were excised from the agarose gel and quantified by Qubit Fluorometer, Agilent 2100 Bioanalyzer and qRT-PCR.

Cellular Antioxidant Activity Assay:

Article Title: Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq
Article Snippet: Nested secondary PCR was performed using indexed SB-2ndR primer (5′- CAA GCA GAA GAC GGC ATA CGA GAT (8 bp index) GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC TTA GGG CTC CGC TTA AGG GAC-3′), SB-RF primer (AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T (1–4 bp stagger) GGC TAA GGT GTA TGT AAA CTT CCG ACT TCA ACT G-3′), and SB-LF primer (AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T (1–4 bp stagger) AAC TTA AGT GTA TGT AAA CTT CCG ACT TCA ACT G-3′). .. DNA fragments between 175 and 450 bp amplicon libraries were excised from the agarose gel and quantified by Qubit Fluorometer, Agilent 2100 Bioanalyzer and qRT-PCR.

ChIP-sequencing:

Article Title: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
Article Snippet: Paragraph title: Chromatin immunoprecipitation sequencing (ChIP-seq) and data analysis ... Libraries were checked with Qubit fluorometer and Bioanalyzer (Agilent) assays and sequenced on the Illumina NextSeq 500 platform to generate single-end 75-bp reads.

DNA Extraction:

Article Title: Consumption of Goats’ Milk Protects Mice From Carbon Tetrachloride-Induced Acute Hepatic Injury and Improves the Associated Gut Microbiota Imbalance
Article Snippet: Paragraph title: Metagenomic DNA Extraction and High-Throughput Sequencing of V3–V4 Regions of 16S rRNA Gene ... The DNA library was quantified using a Qubit Fluorometer and an Agilent Bioanalyzer 2100; sequencing was done using an Illumina HiSeq 2500 System.

Article Title: Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period
Article Snippet: Paragraph title: DNA extraction, PCR amplification and massive sequencing ... The PCR product was purified and concentration and quality were determined for each amplicon using Qubit™ fluorometer and Agilent Bioanalyzer 2100.

RNA Sequencing Assay:

Article Title: Treatment of Human Glioblastoma with a Live Attenuated Zika Virus Vaccine Candidate
Article Snippet: Paragraph title: RNA-seq data acquisition, quality control, and processing. ... The quantities and qualities of the libraries were also assessed by the use of the Qubit Fluorometer and Agilent 2100 Bioanalyzer, respectively, and their molar concentrations were validated by qPCR for library pooling.

Article Title: H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression
Article Snippet: Paragraph title: RNA-sequencing ... The resultant dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and quantitative reverse transcription PCR using the Kapa Biosystems Library Quantification Kit according to the manufacturer’s protocols.

Article Title: A minimal RNA ligand for potent RIG-I activation in living mice
Article Snippet: Paragraph title: RNA-seq library preparation and data analysis ... The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent 2200 TapeStation, and qRT-PCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.

Article Title: NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes
Article Snippet: 2 μg of the DNase-treated total RNA was then subjected to rRNA depletion using the Ribo-Zero Gold (Human/Mouse/Rat) kit and purified again with Ampure XP beads. .. Successful depletion was assessed using a Qubit fluorometer and Agilent 2100 Bioanalyzer and all of the depleted RNA was used for the RNA-Seq library preparation using the ScriptSeq v2 protocol. .. Following 15 cycles of amplification the libraries were purified using Ampure XP beads.

Magnetic Beads:

Article Title: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
Article Snippet: Prepared Pierce Protein A/G Magnetic Beads (Thermo Fisher Scientific) were added to lysates, incubated for 2 h at 4°C, and then washed four times with TBST (25 mM Tris-HCl pH 7.6, 250 mM NaCl, 0.05% Tween-20), once with LiCl Wash Buffer (10 mM Tris-HCl pH 8.0, 0.5M LiCl, 1 mM EDTA, 0.05% Tween-20), once with Lysis Buffer, and once with 1X TE. .. Libraries were checked with Qubit fluorometer and Bioanalyzer (Agilent) assays and sequenced on the Illumina NextSeq 500 platform to generate single-end 75-bp reads.

Isolation:

Article Title: A Systematic Analysis on mRNA and MicroRNA Expression in Runting and Stunting Chickens
Article Snippet: Genomic DNA samples were used for ALV and REV virus detection and isolated from livers by a phenolic extraction protocol. .. Total RNA was tested via agarose electrophoresis, Qubit-fluorometer and Agilent 2100.

Article Title: Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Article Snippet: Total RNA was isolated from BMDMs derived from WT, Arhgef2 −/− , and Irf5 −/− mice, using RNeasy Micro kit (Qiagen). .. The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

Size-exclusion Chromatography:

Article Title: Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period
Article Snippet: The PCR thermal profile consisted of an initial denaturation of 30 sec at 98°C, followed by 30 cycles of 15 sec at 98°C, 15 sec at 55°C, 20 sec at 72°C and a final step of 7 min at 72°C. .. The PCR product was purified and concentration and quality were determined for each amplicon using Qubit™ fluorometer and Agilent Bioanalyzer 2100.

Article Title: Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India
Article Snippet: The adapter tagged DNA was subjected to 12 cycles of indexing-PCR [72°C for 3 min followed by denaturation at 95°C for 30 sec, cycling (95°C for 10 sec, 55°C for 30 sec, 72°C for 30 sec) and 72°C for 5 min] to enrich the adapter-tagged fragments. .. Quantification and size distribution of the prepared libraries were determined using Qubit fluorometer and the Agilent D1000 TapeStation respectively according to the manufacturer’s instructions.

Purification:

Article Title: Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development
Article Snippet: Amplified libraries were purified twice with Agencourt Ampure XP beads (Beckman Coulter, Cat#A63880) with a bead-to-sample ratio of 1.8:1. .. A Qubit fluorometer and Aglient Bioanalyzer were used to check library quality and concentration.

Article Title: Nuclear Transcriptomes at High Resolution Using Retooled INTACT
Article Snippet: After bead capture, DNA was eluted by incubation for 10 min in 50 µL 125 n m NaOH, diluted with 50 µL Tris-HCl (pH 8.8) and purified using AMPure XP beads. .. The quality of the final multiplexed libraries was assessed by use of the Qubit fluorometer and an Agilent Bioanalyzer DNA 1000 assay.

Article Title: H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression
Article Snippet: RNA libraries were prepared using Illumina TruSeq Stranded mRNA Sample Preparation Kits from 500 ng of purified total RNA according to the manufacturer’s protocol. .. The resultant dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and quantitative reverse transcription PCR using the Kapa Biosystems Library Quantification Kit according to the manufacturer’s protocols.

Article Title: Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Article Snippet: Libraries were synthesized using Illumina TruSeq Stranded mRNA sample preparation kit from 500 ng of purified total RNA and indexed adapters according to the manufacturer’s protocol (Illumina). .. The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

Article Title: Consumption of Goats’ Milk Protects Mice From Carbon Tetrachloride-Induced Acute Hepatic Injury and Improves the Associated Gut Microbiota Imbalance
Article Snippet: PCR products were purified using the Qiagen Gel Extraction Kit. .. The DNA library was quantified using a Qubit Fluorometer and an Agilent Bioanalyzer 2100; sequencing was done using an Illumina HiSeq 2500 System.

Article Title: Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period
Article Snippet: To assess possible reagent contamination, each PCR reaction included a no template control (NTC) sample. .. The PCR product was purified and concentration and quality were determined for each amplicon using Qubit™ fluorometer and Agilent Bioanalyzer 2100. .. Barcoded amplicons were sequenced on an Ion Torrent Personal Genome Machine (PGM) with the Ion 318 Chip Kit v2 (Life Technologies) and the Ion PGM™ Sequencing 400 Kit (Life Technologies) under manufacturer’s conditions.

Article Title: A minimal RNA ligand for potent RIG-I activation in living mice
Article Snippet: Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. .. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent 2200 TapeStation, and qRT-PCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.

Article Title: Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India
Article Snippet: The PCR product was purified using HighPrep beads (Magbio Genomics, #AC-60050). .. Quantification and size distribution of the prepared libraries were determined using Qubit fluorometer and the Agilent D1000 TapeStation respectively according to the manufacturer’s instructions.

Article Title: Gene expression plasticity across hosts of an invasive scale insect species
Article Snippet: This mixture was then passed through the standard protocol of the TRIzol® Plus RNA Purification Kit (Thermo Fisher). .. RNA yields and qualities were assessed using a Qubit fluorometer and an Agilent 2100 Bioanalyzer at the Denmark Technical University Multi-Assay Core (DMAC).

Article Title: Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq
Article Snippet: Purified repaired DNA was PCR amplified using linker (5′-GTA ATA CGA CTC ACT ATA GGG C-3′), IRR (5′-GGA TTA AAT GTC AGG AAT TGT GAA AA-3′), and IRL (5′-AAA TTT GTG GAG TAG TTG AAA AAC GA-3′) primers. .. DNA fragments between 175 and 450 bp amplicon libraries were excised from the agarose gel and quantified by Qubit Fluorometer, Agilent 2100 Bioanalyzer and qRT-PCR.

Article Title: NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes
Article Snippet: 2 μg of the DNase-treated total RNA was then subjected to rRNA depletion using the Ribo-Zero Gold (Human/Mouse/Rat) kit and purified again with Ampure XP beads. .. Successful depletion was assessed using a Qubit fluorometer and Agilent 2100 Bioanalyzer and all of the depleted RNA was used for the RNA-Seq library preparation using the ScriptSeq v2 protocol.

Sequencing:

Article Title: Treatment of Human Glioblastoma with a Live Attenuated Zika Virus Vaccine Candidate
Article Snippet: The quantities and qualities of the libraries were also assessed by the use of the Qubit Fluorometer and Agilent 2100 Bioanalyzer, respectively, and their molar concentrations were validated by qPCR for library pooling. .. The quantities and qualities of the libraries were also assessed by the use of the Qubit Fluorometer and Agilent 2100 Bioanalyzer, respectively, and their molar concentrations were validated by qPCR for library pooling.

Article Title: Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling
Article Snippet: The resulting RNA was fragmented and converted into an Illumina sequencing-ready library through ligation, RT, and PCR. .. Prior to sequencing, libraries were evaluated by Qubit fluorometer and TapeStation (Agilent). .. The samples were sequenced using Illumina NextSeq 500 sequencer, at a sequencing depth of an average of 3.5 and 5 million reads per sample for the developmental-seq and perturbations-seq, respectively.

Article Title: Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Article Snippet: The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. .. Pooled libraries were subjected to 35-bp paired-end sequencing according to the manufacturer’s protocol (Illumina NextSeq 500).

Article Title: Consumption of Goats’ Milk Protects Mice From Carbon Tetrachloride-Induced Acute Hepatic Injury and Improves the Associated Gut Microbiota Imbalance
Article Snippet: A TruSeq® DNA PCR-Free Sample Preparation Kit was used to construct the DNA library. .. The DNA library was quantified using a Qubit Fluorometer and an Agilent Bioanalyzer 2100; sequencing was done using an Illumina HiSeq 2500 System. .. The 250 bp paired-end reads were generated through sequencing; the bioinformatics analysis we used for these sequence data has been fully described previously ( , , ).

Article Title: Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period
Article Snippet: Paragraph title: DNA extraction, PCR amplification and massive sequencing ... The PCR product was purified and concentration and quality were determined for each amplicon using Qubit™ fluorometer and Agilent Bioanalyzer 2100.

Article Title: A novel group A rotavirus associated with acute illness and hepatic necrosis in pigeons (Columba livia), in Australia
Article Snippet: Paragraph title: Construction and sequencing of metagenomic libraries ... Final libraries were quantitated on a Qubit Fluorometer and an Agilent Tapestation 2200 before normalising the libraries, and equimolar pooling.

Article Title: Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India
Article Snippet: Paragraph title: Illumina sequencing ... Quantification and size distribution of the prepared libraries were determined using Qubit fluorometer and the Agilent D1000 TapeStation respectively according to the manufacturer’s instructions.

Article Title: Gene expression plasticity across hosts of an invasive scale insect species
Article Snippet: Paragraph title: RNA extraction, library, preparation, and sequencing ... RNA yields and qualities were assessed using a Qubit fluorometer and an Agilent 2100 Bioanalyzer at the Denmark Technical University Multi-Assay Core (DMAC).

Article Title: Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq
Article Snippet: For selective SB insertion site sequencing by HiSeq (Illumina), we modified a published splinkerette PCR protocol . gDNA (3 µg per sample) was acoustically sheared to 200 bp using Covaris S220 Focused-ultrasonicator and end repaired using Fast DNA End Repair Kit (Thermo Fisher Scientific). .. DNA fragments between 175 and 450 bp amplicon libraries were excised from the agarose gel and quantified by Qubit Fluorometer, Agilent 2100 Bioanalyzer and qRT-PCR.

Article Title: NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes
Article Snippet: Paragraph title: RNA-Seq analysis: cDNA library preparation and sequencing ... Successful depletion was assessed using a Qubit fluorometer and Agilent 2100 Bioanalyzer and all of the depleted RNA was used for the RNA-Seq library preparation using the ScriptSeq v2 protocol.

Article Title: Enrichment of PI3K-AKT–mTOR Pathway Activation in Hepatic Metastases from Breast Cancer
Article Snippet: Unstranded mRNA libraries were prepared with 1000 ng of tumor RNA (eRIN > 8) using Illumina TruSeq RNA Library Prep Kit V2. .. All sequencing libraries were quantified and quality assessed with the Qubit Fluorometer and Agilent 2200 TapeStation Instrument, respectively. .. Exome and RNA libraries were paired-end sequenced on the Illumina HiSeq 2500 platform using Rapid Mode with a 109 × 7 × 109 read length.

FACS:

Article Title: Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development
Article Snippet: A Qubit fluorometer and Aglient Bioanalyzer were used to check library quality and concentration. .. A Qubit fluorometer and Aglient Bioanalyzer were used to check library quality and concentration.

Construct:

Article Title: Treatment of Human Glioblastoma with a Live Attenuated Zika Virus Vaccine Candidate
Article Snippet: RNA libraries were constructed using a TruSeq Stranded mRNA Sample Prep kit (Illumina) according to the manufacturer’s guidelines. .. The quantities and qualities of the libraries were also assessed by the use of the Qubit Fluorometer and Agilent 2100 Bioanalyzer, respectively, and their molar concentrations were validated by qPCR for library pooling.

Article Title: Consumption of Goats’ Milk Protects Mice From Carbon Tetrachloride-Induced Acute Hepatic Injury and Improves the Associated Gut Microbiota Imbalance
Article Snippet: A TruSeq® DNA PCR-Free Sample Preparation Kit was used to construct the DNA library. .. The DNA library was quantified using a Qubit Fluorometer and an Agilent Bioanalyzer 2100; sequencing was done using an Illumina HiSeq 2500 System.

Lysis:

Article Title: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
Article Snippet: Prepared Pierce Protein A/G Magnetic Beads (Thermo Fisher Scientific) were added to lysates, incubated for 2 h at 4°C, and then washed four times with TBST (25 mM Tris-HCl pH 7.6, 250 mM NaCl, 0.05% Tween-20), once with LiCl Wash Buffer (10 mM Tris-HCl pH 8.0, 0.5M LiCl, 1 mM EDTA, 0.05% Tween-20), once with Lysis Buffer, and once with 1X TE. .. Libraries were checked with Qubit fluorometer and Bioanalyzer (Agilent) assays and sequenced on the Illumina NextSeq 500 platform to generate single-end 75-bp reads.

cDNA Library Assay:

Article Title: NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes
Article Snippet: Paragraph title: RNA-Seq analysis: cDNA library preparation and sequencing ... Successful depletion was assessed using a Qubit fluorometer and Agilent 2100 Bioanalyzer and all of the depleted RNA was used for the RNA-Seq library preparation using the ScriptSeq v2 protocol.

Sample Prep:

Article Title: Treatment of Human Glioblastoma with a Live Attenuated Zika Virus Vaccine Candidate
Article Snippet: RNA libraries were constructed using a TruSeq Stranded mRNA Sample Prep kit (Illumina) according to the manufacturer’s guidelines. .. The quantities and qualities of the libraries were also assessed by the use of the Qubit Fluorometer and Agilent 2100 Bioanalyzer, respectively, and their molar concentrations were validated by qPCR for library pooling.

Article Title: H3K9 methyltransferases and demethylases control lung tumor-propagating cells and lung cancer progression
Article Snippet: RNA libraries were prepared using Illumina TruSeq Stranded mRNA Sample Preparation Kits from 500 ng of purified total RNA according to the manufacturer’s protocol. .. The resultant dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and quantitative reverse transcription PCR using the Kapa Biosystems Library Quantification Kit according to the manufacturer’s protocols.

Article Title: Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Article Snippet: Libraries were synthesized using Illumina TruSeq Stranded mRNA sample preparation kit from 500 ng of purified total RNA and indexed adapters according to the manufacturer’s protocol (Illumina). .. The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

Article Title: Consumption of Goats’ Milk Protects Mice From Carbon Tetrachloride-Induced Acute Hepatic Injury and Improves the Associated Gut Microbiota Imbalance
Article Snippet: A TruSeq® DNA PCR-Free Sample Preparation Kit was used to construct the DNA library. .. The DNA library was quantified using a Qubit Fluorometer and an Agilent Bioanalyzer 2100; sequencing was done using an Illumina HiSeq 2500 System.

Article Title: A minimal RNA ligand for potent RIG-I activation in living mice
Article Snippet: Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. .. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent 2200 TapeStation, and qRT-PCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.

Activated Clotting Time Assay:

Article Title: Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq
Article Snippet: Nested secondary PCR was performed using indexed SB-2ndR primer (5′- CAA GCA GAA GAC GGC ATA CGA GAT (8 bp index) GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC TTA GGG CTC CGC TTA AGG GAC-3′), SB-RF primer (AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T (1–4 bp stagger) GGC TAA GGT GTA TGT AAA CTT CCG ACT TCA ACT G-3′), and SB-LF primer (AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T (1–4 bp stagger) AAC TTA AGT GTA TGT AAA CTT CCG ACT TCA ACT G-3′). .. DNA fragments between 175 and 450 bp amplicon libraries were excised from the agarose gel and quantified by Qubit Fluorometer, Agilent 2100 Bioanalyzer and qRT-PCR.

Mouse Assay:

Article Title: Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Article Snippet: Total RNA was isolated from BMDMs derived from WT, Arhgef2 −/− , and Irf5 −/− mice, using RNeasy Micro kit (Qiagen). .. The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols.

Chromatin Immunoprecipitation:

Article Title: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
Article Snippet: Ten nanograms of ChIP and input DNA were used to make next-generation sequencing libraries using the NEBNext Ultra II DNA Library Preparation Kit (New England Biolabs). .. Libraries were checked with Qubit fluorometer and Bioanalyzer (Agilent) assays and sequenced on the Illumina NextSeq 500 platform to generate single-end 75-bp reads.

Software:

Article Title: Microbial recognition by GEF-H1 controls IKKε mediated activation of IRF5
Article Snippet: The final dsDNA libraries were quantified by Qubit fluorometer, Agilent Tapestation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. .. Targeted sequencing depth was 30 million paired-end reads per sample.

Real-time Polymerase Chain Reaction:

Article Title: Treatment of Human Glioblastoma with a Live Attenuated Zika Virus Vaccine Candidate
Article Snippet: RNA libraries were constructed using a TruSeq Stranded mRNA Sample Prep kit (Illumina) according to the manufacturer’s guidelines. .. The quantities and qualities of the libraries were also assessed by the use of the Qubit Fluorometer and Agilent 2100 Bioanalyzer, respectively, and their molar concentrations were validated by qPCR for library pooling. .. Libraries were sequenced on a HiSeq X10 platform using the paired-end 2 × 150-bp, dual-index format.

Article Title: NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes
Article Snippet: Successful depletion was assessed using a Qubit fluorometer and Agilent 2100 Bioanalyzer and all of the depleted RNA was used for the RNA-Seq library preparation using the ScriptSeq v2 protocol. .. Successful depletion was assessed using a Qubit fluorometer and Agilent 2100 Bioanalyzer and all of the depleted RNA was used for the RNA-Seq library preparation using the ScriptSeq v2 protocol.

RNA Extraction:

Article Title: A Systematic Analysis on mRNA and MicroRNA Expression in Runting and Stunting Chickens
Article Snippet: Paragraph title: 4.3. Liver DNA and RNA extraction ... Total RNA was tested via agarose electrophoresis, Qubit-fluorometer and Agilent 2100.

Article Title: Gene expression plasticity across hosts of an invasive scale insect species
Article Snippet: Paragraph title: RNA extraction, library, preparation, and sequencing ... RNA yields and qualities were assessed using a Qubit fluorometer and an Agilent 2100 Bioanalyzer at the Denmark Technical University Multi-Assay Core (DMAC).

Article Title: NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap4A) and Down-Regulates Immune Response and Cancer Promotion Genes
Article Snippet: RNA extraction was performed using a Qiagen RNeasy mini kit with QIAshredder, and the quantity and quality determined using a Nanodrop and Agilent Bioanalyzer. .. Successful depletion was assessed using a Qubit fluorometer and Agilent 2100 Bioanalyzer and all of the depleted RNA was used for the RNA-Seq library preparation using the ScriptSeq v2 protocol.

Agarose Gel Electrophoresis:

Article Title: Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq
Article Snippet: All oligos were purchased from Integrated DNA Technologies with Standard Desalting. .. DNA fragments between 175 and 450 bp amplicon libraries were excised from the agarose gel and quantified by Qubit Fluorometer, Agilent 2100 Bioanalyzer and qRT-PCR. .. Excised libraries were then pooled, loaded onto two flow cell lanes and sequenced on the Hiseq2500 platform.

In Vitro:

Article Title: Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling
Article Snippet: In brief, mRNA was barcoded, converted into cDNA and linearly amplified by T7 in vitro transcription. .. Prior to sequencing, libraries were evaluated by Qubit fluorometer and TapeStation (Agilent).

Next-Generation Sequencing:

Article Title: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
Article Snippet: Ten nanograms of ChIP and input DNA were used to make next-generation sequencing libraries using the NEBNext Ultra II DNA Library Preparation Kit (New England Biolabs). .. Libraries were checked with Qubit fluorometer and Bioanalyzer (Agilent) assays and sequenced on the Illumina NextSeq 500 platform to generate single-end 75-bp reads.

Concentration Assay:

Article Title: Treatment of Human Glioblastoma with a Live Attenuated Zika Virus Vaccine Candidate
Article Snippet: The RNA concentration was quantified using a Qubit 2.0 Fluorometer (Thermo Fisher), and the quality of the extracted RNA was evaluated using an Agilent Technology 2100 Bioanalyzer. .. The quantities and qualities of the libraries were also assessed by the use of the Qubit Fluorometer and Agilent 2100 Bioanalyzer, respectively, and their molar concentrations were validated by qPCR for library pooling.

Article Title: Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development
Article Snippet: Amplified libraries were purified twice with Agencourt Ampure XP beads (Beckman Coulter, Cat#A63880) with a bead-to-sample ratio of 1.8:1. .. A Qubit fluorometer and Aglient Bioanalyzer were used to check library quality and concentration. .. Libraries were 50 bp single-end sequenced on Illumina HiSeq 2500 platform to a depth of (3.5–7.0) × 107 reads.

Article Title: Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period
Article Snippet: To assess possible reagent contamination, each PCR reaction included a no template control (NTC) sample. .. The PCR product was purified and concentration and quality were determined for each amplicon using Qubit™ fluorometer and Agilent Bioanalyzer 2100. .. Barcoded amplicons were sequenced on an Ion Torrent Personal Genome Machine (PGM) with the Ion 318 Chip Kit v2 (Life Technologies) and the Ion PGM™ Sequencing 400 Kit (Life Technologies) under manufacturer’s conditions.

High Throughput Screening Assay:

Article Title: Consumption of Goats’ Milk Protects Mice From Carbon Tetrachloride-Induced Acute Hepatic Injury and Improves the Associated Gut Microbiota Imbalance
Article Snippet: Paragraph title: Metagenomic DNA Extraction and High-Throughput Sequencing of V3–V4 Regions of 16S rRNA Gene ... The DNA library was quantified using a Qubit Fluorometer and an Agilent Bioanalyzer 2100; sequencing was done using an Illumina HiSeq 2500 System.

Gel Extraction:

Article Title: Consumption of Goats’ Milk Protects Mice From Carbon Tetrachloride-Induced Acute Hepatic Injury and Improves the Associated Gut Microbiota Imbalance
Article Snippet: PCR products were purified using the Qiagen Gel Extraction Kit. .. The DNA library was quantified using a Qubit Fluorometer and an Agilent Bioanalyzer 2100; sequencing was done using an Illumina HiSeq 2500 System.

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    Agilent technologies qubit 2 0 fluorometer
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    Agilent technologies qubit fluorometer system
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