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73 protocols using maxwell 16 lev blood dna kit

1

Extracting RNA and DNA from Uterus Tissue

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RNA was isolated from uterus tissue samples using the Maxwell 16 Tissue LEV Total RNA Purification Kit (Promega GmbH, Mannheim, Germany) according to the manufacturer’s instructions. The reverse transcription of messenger RNA (mRNA) into cDNA was performed using the GoScript Reverse Transcription System (Promega GmbH) according to the technical manual.
For extraction of genomic DNA from uterus tissue samples, we used the Maxwell 16 LEV Blood DNA Kit (Promega GmbH) with a modified lysis protocol (crushing a piece of tissue of ∼5 mm in diameter, incubation at 56° for 2 hr with 400 µl lysis buffer and 40 µl proteinase K). Extraction of genomic DNA from hair roots was also performed using the Maxwell 16 LEV Blood DNA Kit (Promega GmbH) and the same modified lysis protocol as described above, omitting the crushing step.
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2

Automated DNA Extraction from Blood

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DNA was extracted using the Maxwell 16 LEV Blood DNA kit (Promega) and the automated Maxwell 16 device (AS1000; Promega) per the manufacturer's instructions. In each extraction batch of 15 samples, a negative extraction control (NEC; lysis buffer only) was included.
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3

Pharmacogenomic Genotyping Protocol

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Buffy coats were prepared from 9 mL whole‐blood EDTA samples after plasma separation. Genomic DNA was extracted from the buffy coats using the Maxwell 16 LEV Blood DNA Kit on a Maxwell 16 Research automated nucleic acid extraction system (Promega, Madison, WI). The participants were genotyped for the CYP2C8*2 (rs11572103), *3 (rs10509681 and rs11572080), and *4 (rs1058930), CYP2C19*2 (rs4244285), *3 (rs4986893), *8 (rs41291556), and *17 (rs12248560), UGT1A3*2 (rs3821242 and rs6431625), *3 (rs3821242), and *6 (rs3821242, rs6431625, and rs45449995), and CES1 c.428G>A (rs71647871) alleles with commercially available or custom TaqMan assays with OpenArray technology on a QuantStudio 12K Flex real‐time polymerase chain reaction system (Life Technologies, Carlsbad, CA).
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4

Whole-Genome Sequencing of Leukocytes

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Whole‐genome sequencing (WGS) was conducted on DNA sample extracted from whole leukocytes of peripheral blood obtained from the patient before imatinib therapy. Genomic DNA was extracted from the whole blood using Maxwell® 16 LEV Blood DNA Kit (Promega, Fitchburg, WI), sheared into approximately 350 bp fragments, and used to make a library with TruSeq Nano DNA Sample Prep Kit (Illumina, San Diego, CA). Sequencing was performed on an Illumina HiSeq X platform in paired‐end 150 bp configuration.
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5

Sensitive Skin Microbiome Analysis

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The first D-Squame Skin Stripping disc in 300 μL 1X DNA/RNA shield was subjected to extraction with the Maxwell 16 LEV Blood DNA kit (Promega, Netherlands) as specified in the manufacturer’s manual using the automated Maxwell 16 Instrument (AS1000, Promega). Nucleic acids were subsequently tested by qPCR targeting kinetoplast DNA (kDNA) as described by Merdekios et al. (17 (link)). The specific primers and probes used were LC-F (5’-TATTTTACACCAACCCCCAGT-3′), LC-R (5’-GGTAGGGGCGTTCTGC-3′) and a FAM-labeled LC-probe (5’-CAGAAAYCCCGTTCAAAAAATGGC-3′). If a sample was negative, the second D-Squame Skin Stripping disc was tested. If there was still no fluorescence, an HBB PCR was performed as described by Steinau et al. (18 (link)) to assess if there was sufficient tissue on the discs and whether the DNA extraction was conducted successfully.
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6

Salmonella Agona Genomic DNA Isolation

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Salmonella Agona isolates were freshly grown on blood agar plates. One inoculation loop of bacterial material was suspended in 50 µL phosphate buffered saline (PBS) and cells were pre-treated with 1 µg lysozyme for 15 min at 37 °C followed by a 2 hour incubation step at 65 °C with 200 µL incorporation buffer, 200 µL lysis buffer, 30 µL 20 mg/mL Proteinase K and 10 µL 10 mg/mL ribonuclease (RNase) A (all reagents from Promega, Mannheim, Germany). Genomic DNA (gDNA) was then isolated with the Maxwell 16 LEV Blood DNA Kit on the Maxwell 16 instrument (Promega, Mannheim, Germany) according to manufacturer’s instructions with Tris buffer for gDNA elution.
Whole genome libraries for NGS were prepared using the Nextera XT kit (Illumina, San Diego, California, US). Next generation sequencing was performed on the Illumina MiSeq with 2x250 bp paired-end reads. Sequencing runs were evaluated for quality using the Illumina SAV Software.
Sequencing data were uploaded to the NCBI sequence read archive (SRA) [26 ], under BioProject PRJNA473689.
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7

DNA and RNA Extraction from Blood

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DNA extraction was performed with the Maxwell® 16 LEV Blood DNA Kit (Promega, Charbonnières-les-Bains, France) on EDTA blood samples according to the manufacturer’s instructions. RNA was directly extracted from 5 mL of PAXgeneTM blood samples with the PAXgeneTM Blood RNA System (Qiagen, Courtaboeuf, France) according to the manufacturer’s instructions. DNA concentrations were quantified using a NanoDrop 1000 Spectrophotometer v3.8 (Thermo Fisher Scientific, Courtaboeuf, France).
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8

HLA Typing of Glioma Patient Samples

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Genomic DNA was isolated from patient blood and glioma tissue using the NucleoSpin Tissue Kit (Macherey-Nagel) or the Maxwell® 16 LEV Blood DNA Kit (Promega). The isolated DNA was HLA-typed as described previously.24 (link)
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9

Plasma gDNA Extraction and Quantification

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gDNA was extracted from plasma samples using Maxwell 16 LEV Blood DNA Kit (Promega, Madison, WI, #AS1290). Concentrations were measured using Qubit 4 Fluorometer (ThermoFisher Scientific, Waltham, MA) or Quantus Fluorometer (Promega) calibrated with double stranded DNA (ThermoFisher Scientific). Samples with concentrations below 0.3 ng/μl, or that were cloudy were amplified and repaired using the whole genome amplification REPLI-g FFPE Kit (Qiagen, Germantown, MD).
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10

Quantifying Lentiviral Vector Persistence

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Briefly, 1 million mouse splenocytes were harvested and genomic DNA extracted by ACGT, Inc. using the Promega Maxwell® 16 LEV Blood DNA Kit. To determine CAR-T persistence, a unique fragment (c-frag) contained within the lentiviral vector backbone of anti-HIV CARs, but not the HIV-1 virus, was used to assess copy numbers per 50 ng of genomic DNA isolated from mouse splenocytes. The following primers and probe were used to detect c-frag: Forward primer: 5’GGAGTTGAGACCAGTGTAGT-3’, Reverse primer: 5’-CCACTCCTGACAACTACTCT-3’, Probe: 5’-FAM-CAGTAGGTGAAGGAGTCGTAGTTG-TAMRA-3’. The following primers and probe were used to detect the polypyrimidine tract binding protein 2 (PTBP2) gene to control for PCR inhibition: Forward primer: 5’-TCTCCATTCCCTATGTTCATGC-3’, Reverse primer: 5’-GTTCCCGCAGAATGGTGAGGTG-3’, Probe: 5’-JOE-ATGTTCCTCGGACCAACTTG-BHQ-1-3’. The PTBP2 gene was used as an internal control to assess PCR inhibition. The number of cFrag copies in splenic DNA was calculated using a standard curve consisting of known quantities of a plasmid DNA containing the c-frag genetic tag followed by normalization to input splenic DNA (0.05 μg) multiplied by the volume of the reaction added per well (12.5 μL).
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