RNA was isolated using the RNeasy Mini kit (Qiagen, 74106). The amount of total RNA was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amount was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). Libraries were pooled, diluted and sequenced using the Illumina HiSeq3000/4000 platform with the 50 bp single-read configuration.
Qubit 2.0 fluorometric quantitation system
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Qubit 2.0 Fluorometric Quantitation system is a compact, easy-to-use device designed for accurate and sensitive measurement of DNA, RNA, and protein concentrations. It utilizes fluorescent dye-based technology to quantify the target molecule in a small sample volume. The system provides reliable results with a wide dynamic range and minimal sample requirement.
Automatically generated - may contain errors
Lab products found in correlation
Experion automated electrophoresis system, by Bio-Rad (12 mentions)
Truseq stranded mrna lt sample preparation kit, by Illumina (10 mentions)
Rneasy mini kit, by Qiagen (5 mentions)
Sciclone and zephyr liquid handling workstations, by PerkinElmer (5 mentions)
Sciclone and zephyr liquid handling robotics, by PerkinElmer (3 mentions)
Hiseq 3000 4000 platform, by Illumina (2 mentions)
Hiseq 3000 4000 instruments, by Illumina (2 mentions)
Qubit dsdna hs assay, by Thermo Fisher Scientific (2 mentions)
Hiseq 3000 4000 machines, by Illumina (2 mentions)
Real time analysis software, by Illumina (1 mentions)
Hiseq 3000 4000, by Illumina (1 mentions)
Qiazol, by Qiagen (1 mentions)
Dnase digestion, by Qiagen (1 mentions)
Hiseq 4000, by Illumina (1 mentions)
Truseq rna sample kit, by Illumina (1 mentions)
S220 focused ultrasonicator instrument, by Covaris (1 mentions)
Truseq dna pcr free ht library prep kit, by Illumina (1 mentions)
Idt for truseq ud indexes, by Illumina (1 mentions)
Quantseq 3 mrna seq library prep kit, by Lexogen (1 mentions)
Hiseq 2000 machine, by Illumina (1 mentions)
18 protocols using qubit 2.0 fluorometric quantitation system
1
RNA Sequencing Library Preparation
2
RNA-seq Library Preparation Workflow
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RNA from two independent replicates, originating from the same cell pools as the corresponding ATAC-seq samples, was isolated using the RNeasy Mini kit (catalog no. 74106; QIAGEN). The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). Individual samples were diluted and pooled into NGS libraries in equimolar amounts. Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-bp single-end mode.
3
RNA-seq Library Preparation and Quantification
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The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA), and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA), and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.
4
RNA Sequencing Library Preparation
5
RNA-seq library preparation and sequencing
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The amount of total RNA was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amount was quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing 6 libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 75 bp paired-end chemistry. Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam ).
6
RNA-seq Library Preparation Workflow
7
RNA-seq Library Preparation and Quantification
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The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using both, Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.
8
RNA-Seq Library Preparation and Quantification
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Total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into next generation sequencing (NGS) libraries in equimolar amounts.
9
RNA-seq Library Preparation and Sequencing
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The total RNA amount was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA), and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA). The size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.
10
RNA-seq Library Preparation Workflow
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Total RNA was extracted using QIAzol (79306; Qiagen, Germany), followed by DNAse digestion (Qiagen, Germany) treatment on the RNeasy Mini columns, according to the manufacturer’s protocol. The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA), and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA). The size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.
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