DNA was extracted from plasma and urine using the QIAamp Circulating Nucleic Acid Kit according to the manufacturer’s instructions (Qiagen, Cat #55114). Sequencing libraries were prepared using a single-stranded library preparation as described in Burnham et al.13 (link). DNA was extracted from oral swab samples using the QIAamp UCP Pathogen Kit according to the manufacturer’s instructions (Qiagen, Cat #50214) and libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina, Cat #FC-131-1024). All libraries were characterized using the AATI Fragment Analyzer before pooling and sequencing on the Illumina NextSeq 500 platform (paired-end, 2 × 75 bp).
Qiaamp ucp pathogen kit
Manufactured by Qiagen
Sourced in Germany
The QIAamp® UCP Pathogen Kit is a laboratory tool designed for the rapid and efficient extraction of nucleic acids from a variety of sample types, including clinical and environmental samples. The kit utilizes QIAGEN's proprietary UltraPure™ technology to provide high-quality nucleic acid purification, enabling downstream applications such as PCR, sequencing, and other molecular biology analyses.
Automatically generated - may contain errors
Lab products found in correlation
Nextseq 550dx platform, by Illumina (3 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (3 mentions)
Nanodrop, by Thermo Fisher Scientific (2 mentions)
Qubit fluorometer, by Thermo Fisher Scientific (2 mentions)
Fragment analyzer, by Illumina (1 mentions)
Nextera xt dna library prep kit, by Illumina (1 mentions)
Qiaamp circulating nucleic acid kit, by Qiagen (1 mentions)
Nextseq 500 platform, by Illumina (1 mentions)
5 protocols using qiaamp ucp pathogen kit
1
Circulating DNA Sequencing Protocol
2
Sputum DNA Extraction for TB Detection
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Sputum samples from TB patients and induced sputum from HVs were heat-inactivated for 20 min at 80 °C, pretreated with 500 mg of N-acetyl-l -cysteine for 15 min and two volumes of NaOH 2.0% for 10 min, with two intermediate shaking sessions. PBS was added to the mixture for a final volume of 50 mL, and two steps of centrifugation were performed. First, the pellet was resuspended with 10 mL of deionized sterile water and incubated for 30 min. After the second centrifugation, the sample was resuspended in 1.5 mL deionized sterile water. DNA extraction was performed using the QIAamp UCP pathogen kit (Qiagen, Hilden, Germany,) following the manufacturer’s instructions. Purified DNA was diluted to a final concentration of 50 ng/µL and stored at −20 °C. DNA integrity was verified by agarose gel electrophoresis and quantified spectrophotometrically using Nanodrop (Thermo Scientific, Wilmington, DE, USA).
3
Extraction and Library Preparation of Cell-Free DNA for Sequencing
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DNA was extracted using the QIAamp® UCP Pathogen Kit (Qiagen, Germany) according to the manufacturer’s protocol. Cell-free DNA (cfDNA) from plasma samples was extracted by using the TIANamp Micro DNA DP316 Kit (Tiangen Biotech, Beijing, China) following the manufacturer’s recommendations.
The extracted DNA samples were used to construct DNA libraries by using the TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, Nanjing, China). cfDNA samples were used to construct DNA libraries by using the VAHTS Universal DNA Library Prep Kit V3 for Illumina® (Vazyme, Nanjing, China). All libraries were prepared following the manufacturer’s manuals. The Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) was used for library quality control. All libraries were pooled with other libraries by using different index sequences and sequenced on an Illumina NextSeq 550Dx platform with the single-end 75bp sequencing option. For each run, no-template control (NTC) samples (Nuclease-free H2O) were also pooled to monitor reagent and laboratory background.
The extracted DNA samples were used to construct DNA libraries by using the TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, Nanjing, China). cfDNA samples were used to construct DNA libraries by using the VAHTS Universal DNA Library Prep Kit V3 for Illumina® (Vazyme, Nanjing, China). All libraries were prepared following the manufacturer’s manuals. The Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) was used for library quality control. All libraries were pooled with other libraries by using different index sequences and sequenced on an Illumina NextSeq 550Dx platform with the single-end 75bp sequencing option. For each run, no-template control (NTC) samples (Nuclease-free H2O) were also pooled to monitor reagent and laboratory background.
4
Cerebrospinal Fluid DNA Extraction and Sequencing
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At least 1 mL CSF samples were collected from patients according to the standard clinical procedure. DNA was extracted using the QIAamp® UCP Pathogen Kit (Qiagen, Germany) according to the manufacturer’s recommendations. The extracted DNA samples were quantified using a Qubit fluorometer (Thermo Fisher Scientific, CA, United States).
DNA libraries were prepared using the TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, Nanjing, China) according to the manufacturer’s instructions in the manual. An Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, United States) was used for assessing library quality control. All libraries were pooled with other libraries using different index sequences and sequenced on an Illumina NextSeq 550Dx platform with a single-end 75-bp sequencing option. For each run, no template control (NTC) samples (nuclease-free H2O) were also pooled to monitor the reagent and laboratory background.
DNA libraries were prepared using the TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, Nanjing, China) according to the manufacturer’s instructions in the manual. An Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, United States) was used for assessing library quality control. All libraries were pooled with other libraries using different index sequences and sequenced on an Illumina NextSeq 550Dx platform with a single-end 75-bp sequencing option. For each run, no template control (NTC) samples (nuclease-free H2O) were also pooled to monitor the reagent and laboratory background.
5
BALF DNA and RNA Extraction and Sequencing
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6-10ml BALF samples were collected from patients according to the standard clinical procedure. DNA from BALF samples was extracted using the QIAamp® UCP Pathogen Kit (Qiagen, Germany) according to the manufacturer’s recommendations. RNA from BALF samples was extracted using the TIANamp Virus RNA DP315-R Kit (Tiangen Biotech, Beijing, China) following the manufacturer’s instructions.
The extracted DNA samples were used to construct DNA libraries by using the TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, Nanjing, China). RNA libraries were prepared from the extracted RNA samples by using the VAHTS Universal RNA-seq Library Prep Kit V6 for Illumina® (Vazyme, Nanjing, China). All libraries were prepared following the manufacturer’s manuals. The Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) was used for library quality control. All libraries were pooled with other libraries by using different index sequences and sequenced on an Illumina NextSeq 550Dx platform with the single-end 75bp sequencing option. For each run, negative control (NC) samples (Nuclease-free H2O) were also pooled to monitor reagent and laboratory background.
The extracted DNA samples were used to construct DNA libraries by using the TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, Nanjing, China). RNA libraries were prepared from the extracted RNA samples by using the VAHTS Universal RNA-seq Library Prep Kit V6 for Illumina® (Vazyme, Nanjing, China). All libraries were prepared following the manufacturer’s manuals. The Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) was used for library quality control. All libraries were pooled with other libraries by using different index sequences and sequenced on an Illumina NextSeq 550Dx platform with the single-end 75bp sequencing option. For each run, negative control (NC) samples (Nuclease-free H2O) were also pooled to monitor reagent and laboratory background.
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