Tumor DNA was extracted from FFPE tissues using the QIAamp DNA FFPE Tissue Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendation. Blood DNA was extracted from whole blood using the Gentra Puregene Blood Kit (Qiagen, Hilden, Germany) or the QIAsymphony DSP DNA Kits (Qiagen, Hilden, Germany) according to the manufacturers’ protocols.
Qiasymphony dsp dna kit
Manufactured by Qiagen
Sourced in Germany
The QIAsymphony DSP DNA kit is a laboratory instrument designed for automated extraction and purification of DNA from various sample types. It utilizes magnetic bead technology to efficiently isolate high-quality DNA for downstream applications.
Automatically generated - may contain errors
Lab products found in correlation
Gentra puregene blood kit, by Qiagen (2 mentions)
Qiasymphony sp, by Qiagen (2 mentions)
Qiasymphony sp instrument, by Qiagen (2 mentions)
Dsp dna mini kit, by Qiagen (2 mentions)
Nanodrop spectrophotometer, by Thermo Fisher Scientific (2 mentions)
Qiaamp dna ffpe tissue kit, by Qiagen (1 mentions)
Infinium methylationepic beadchip microarray, by Illumina (1 mentions)
Genomestudio software, by Illumina (1 mentions)
Ez dna methylation kit, by Zymo Research (1 mentions)
Nuclease free water, by Promega (1 mentions)
Qiamp circulating nucleic acid kit, by Qiagen (1 mentions)
Mo bio power fecal dna isolation kit, by Qiagen (1 mentions)
Qubit dsdna high sensitivity kit, by Thermo Fisher Scientific (1 mentions)
Dneasy blood and tissue kit, by Qiagen (1 mentions)
Qiasymphony circulating nucleic acid kit, by Qiagen (1 mentions)
Qiasymphony automated nucleic acid extraction facility, by Qiagen (1 mentions)
Lysostaphin solution, by Merck Group (1 mentions)
Qiasymphony, by Qiagen (1 mentions)
Ion onetouch 2 system, by Thermo Fisher Scientific (1 mentions)
Ion onetouch es, by Thermo Fisher Scientific (1 mentions)
17 protocols using qiasymphony dsp dna kit
1
DNA Extraction from FFPE and Blood
2
PBMC Genome-wide DNA Methylation Profiling
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The method for profiling genome-wide DNAm in peripheral blood mononuclear cells (PBMCs) in the CLSA participants has been described in the CLSA Data Support Document (David et al., 2020) . Briefly, the proportion of methylation on CpG nucleotide base pairs on the DNA extracted from the PBMCs was measured using the Illumina Infinium MethylationEPIC BeadChip microarrays referred to as the EPIC arrays (Illumina, CA, USA). The EPIC array quantitatively measures DNAm at 862,927 CpG sites and 2,932 CHH sites across the genome. To obtain the DNAm data, genomic DNA were extracted from the frozen PBMC samples using QIAsymphony DSP DNA Kits (Qiagen, Hilden, GE), and bisulfite conversion using the EZ DNA Methylation kit (Zymo, CA, USA) was performed. The resulting bisulfite-converted DNA was processed on the EPIC arrays following manufacturer's instructions. For Quality control purposes, these raw array data were preprocessed using the GenomeStudio software (Illumina, CA, USA), which transformed the raw methylation values into beta values. The beta values range from 0 to 1 and indicate the proportion of methylation at each CpG loci present in the sample.
3
Plasma, Fecal, and Saliva DNA Extraction
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Plasma DNA was extracted from up to 2 ml of plasma using the QIAmp Circulating Nucleic Acid Kit (Qiagen) according to the manufacturer’s instructions. All plasma DNA extractions were performed under sterile conditions (using disposable surgical gown and gloves) in a Biosafety Level 2 cabinet dedicated only to plasma DNA extractions in which all equipment had been disinfected and DNA-cleaned using 70% ethanol, 1% Virkon, DNA decontamination reagent (Sigma LookOut DNA Erase) and UV light for a minimum of 30 min. The plasma DNA was eluted into 50 μl buffer AVE and stored at − 20 °C. Faecal specimens were extracted for DNA using the MoBio PowerFecal DNA isolation kit (Qiagen) according to the manufacturer’s instructions and stored at − 20 °C. Saliva samples were extracted for DNA using the Qiasymphony SP and the QIAsymphony DSP DNA Kit (Qiagen). DNA Extraction Negative Controls (DENC) were employed where nuclease-free water (Promega) was the only input performed in each extraction to assess for possible contamination arising from the different extraction kits. E. coli derived DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer’s protocols, quantified using the Qubit high-sensitivity dsDNA kit (Thermo Fisher Scientific) and diluted in nuclease-free water for the dilution series.
4
Isolation and Extraction of Maternal Cell-Free DNA
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Maternal and control plasma was isolated from 10 mL blood samples received in Streck (La Vista, USA) BCT tubes and stored at −80 °C. Cell-free DNA was extracted either from 4 mL of plasma using the QIAsymphony Circulating Nucleic Acid kit (Qiagen, Hilden, Germany) into a final volume of 60 μL AVE buffer or from 2 mL plasma using a QIAamp DSP MiniElute virus kit (Qiagen, Hilden, Germany) into a final volume of 50 μL AVE buffer. Genomic DNA (gDNA) was extracted from leukocytes by QIAsymphony DSP DNA kit (Qiagen, Hilden, Germany).
5
Selective Whole Genome Amplification from Dried Blood Spots
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DNA from isolates collected in years 2015 and 2016 was extracted in 2021 from dried-blood spots (DBS) preserved on filter papers. Filter papers were stored at 4 °C from 2015/2016 until blood extraction in 2021. A cold chain was not maintained during sample shipment from Kenya to the London School of Hygiene and Tropical Medicine. For DNA extraction, half of a DBS was used. DNA extraction was performed using the Qiagen QiaSymphony Automated Nucleic Acid Extraction Facility and the Qiagen QIAsymphony DSP DNA kit. Following extraction, DNA was amplified using an established selective whole genome amplification (SWGA) primer set and protocols31 (link),47 (link).
6
Whole-Genome Sequencing of Labrador Retrievers
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A family quartet of Labrador retriever dogs (sire, dam, and two affected offspring numbered LAB1, LAB2, LAB3, and LAB4, respectively) were used in the whole-genome sequencing (WGS). In addition, 16 related individuals (LAB5 to LAB20, see S1 Fig
7
Automated Bacterial DNA Extraction Protocol
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Bacterial isolates were cultivated overnight according to the propagation procedure of the supplier (Microbiologics, MN, United States). Automated DNA extraction from Gram-positive and Gram-negative bacteria was performed on a QIAsymphony instrument (QIAGEN, Hilden, Germany) using the QIAsymphony DSP DNA Kit (QIAGEN). Modifications of the manufacturers standard protocol included: for extraction from S. aureus addition of lysostaphin solution (5 U per sample; Sigma-Aldrich, St. Louis, MO, United States); lysis of Gram-positive bacteria on device (37°C/shaking at 900 rpm for 1 h); a third wash step to enhance purification for extraction of Gram-positive and Gram-negative bacteria. Each independent DNA extraction contained a no template control (NTC) containing molecular grade water only.
8
Chinese Crested Dog Genomic DNA Sequencing
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Genomic DNA from four Chinese Crested dogs was extracted from peripheral blood leukocytes, using 1 ml blood on a QIAsymphony SP instrument and the QIAsymphony DSP DNA Kit (Qiagen, Hilden, Germany). One microgram of genomic DNA was fragmented using the Covaris S2 instrument (Covaris, Inc. Woburn, MA) and library preparation was performed using the Ion Xpress™ Plus Fragment Library Kit for AB Library Builder™ System followed by five cycles of amplification. Emulsion PCR was done on the Ion OneTouch™ 2 system with Ion PI™ Template OT2 200 Kit v2 chemistry (Life Technologies, Thermo Fisher Scientific, Waltham, MA). Enrichment was conducted using the Ion OneTouch™ ES (Life Technologies). Samples were loaded on two Ion PI™ chips Kit v2 and sequenced on the Ion Proton™ System using Ion PI™ Sequencing 200 Kit v2 chemistry (200 bp read length, Life Technologies).
Reads were aligned to the canine reference genome sequence (CanFam3.1.) using TorrentSuit 3.6 software with default settings. We further assessed the quality of obtained alignments using standalone versions of FastQC v0.7.2 [26 ].
Reads were aligned to the canine reference genome sequence (CanFam3.1.) using TorrentSuit 3.6 software with default settings. We further assessed the quality of obtained alignments using standalone versions of FastQC v0.7.2 [26 ].
9
Canine Paw Pad Hyperkeratosis Study
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Kromfohrländer dogs were recruited via the breed association and breeders of Kromfohrländer dogs. A boarded veterinary dermatologist clinically examined the dogs. Pedigrees from all dogs were collected. Dogs with a history of hyperkeratosis affecting all four paw pads since juvenility, and with clinical lesions compatible with the disease, with hyperkeratotic, firm and cracking pads were diagnosed as cases, whereas dogs with clinically normal paw pads were included as healthy controls. Biopsies, when taken from cases, revealed histopathological changes typical for paw pad hyperkeratosis. All samples were obtained with informed dog owner consent. Ethical approval was granted by the Swedish Animal Ethical Committee Dnr C12/15.
Whole blood was collected from nine cases and 18 healthy Kromfohrländer dogs into EDTA tubes. Genomic DNA was extracted from peripheral blood leukocytes, using 1 ml blood on a QIAsymphony SP instrument using the QIAsymphony DSP DNA Kit (Qiagen, Hilden, Germany).
Whole blood was collected from nine cases and 18 healthy Kromfohrländer dogs into EDTA tubes. Genomic DNA was extracted from peripheral blood leukocytes, using 1 ml blood on a QIAsymphony SP instrument using the QIAsymphony DSP DNA Kit (Qiagen, Hilden, Germany).
10
Robust FFPE DNA Extraction Protocol
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Tumour DNA was isolated from two 10 µm whole slides of formalin-fixed paraffin-embedded (FFPE) tissue containing at least 50% tumour cells. Manual microdissection was carried out for slides containing ≤50% of representative tumour area to increase the percentage of neoplastic cells. Paraffin was removed with Qiagen’s Deparaffinization Solution, and tissue was lysed using a mixture of 20 μL Proteinase K (20 mg/ml, included in the QIAsymphony DSP DNA kit) and 200 μL lysis buffer (0.05 M Tris-HCl ph 8.5, 0.04 mM EDTA, 0.5% Tween20) per sample at 56 °C overnight. DNA extraction was performed with QIAsymphony SP instrument using DSP DNA mini kit with 100 µL elution volume (Qiagen, Venlo, The Netherlands).
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