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6 protocols using vacuum manifold

1

Plasma cfDNA Extraction Protocol

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Cell‐free DNA was extracted from 4 mL or 8 mL of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Cat No 55114, Valencia, CA, USA), with a Qiagen vacuum manifold following the manufacturers’ instructions. cfDNA was then eluted in a final volume of 60‐110 µL elution buffer (AVE), depending on the volume of plasma used for the extraction (4 mL or 8 mL).10
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2

Total RNA Extraction from Cell Lines

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Total RNA extractions from monolayers of LLC-MK2 cells and HREC monolayer, and organotypic ALI-HRECs were performed with TRIzol reagent (Thermo Fisher Scientific) using the E.Z.N.A. Total RNA Kit (Omega Bio-tek, Inc., Norcross, GA USA) and vacuum manifold (Qiagen) method following the manufacturer’s instructions. Eluted RNA was quantified using a NanoDrop one microvolume UV-Vis spectrophotometer (Thermo Fisher Scientific). Samples with A260/280 between 1.96 and 2.05 were used for cDNA synthesis from 40 ng of total RNA per sample using qScript XLT cDNA SuperMix kit (QuantaBio, Beverly, MA, USA) and then stored at −20°C.
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3

Isolation of Extracellular Vesicles from 4T1 Cells

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EV-depleted FBS was prepared by 18 h-ultracentrifugation at 100,000g, 4 °C [31 ]. 4T1 cells were seeded at 7 × 105 cells or 1.5 × 106 cells per 60 mm or 100 mm cell culture dishes respectively, and cultured in the EV-depleted medium, and microvesicles were then harvested as described previously [14 (link)]. Briefly, conditioned medium was centrifuged at 600 × g for 30 min to remove cells and debris. The supernatant was centrifuged again at 2,000 × g for 30 min to remove apoptotic bodies. Microvesicles were collected by ultracentrifugation at 20,000 × g for 60 min using Optima XL-90 Ultracentrifuge and 90Ti rotor (Beckman Coulter), or refrigerated microcentrifuge 5424 R (Eppendorf) for small volumes. Supernatants were filtered through 0.22-μm membrane filters (Thermo Scientific) with pressure to remove large vesicles. Exosomes were collected by a size-based EV isolation method with modifications [32 (link)] using 50 nm membrane filters (EMD Millipore, VMWP02500) with holders (EMD Millipore, SX0002500). Briefly, holders with 50 nm membrane filters were connected to a vacuum manifold (Qiagen), and the membrane filters were first washed with 5 – 10 mL of PBS buffer by applying vacuum. Then, the remaining EVs including exosomes in the supernatant were trapped on the membranes. When ~100 μL of sample remained, the concentrated EVs were carefully collected.
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4

PHEV Viral RNA Extraction and RT-qPCR Detection

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Viral RNA extractions were performed using the E.Z.N.A. viral RNA kit (Omega Bio-tek, Inc., Norcross, GA, USA) and vacuum manifold (Qiagen, Germantown, MD, USA) method following the manufacturer’s instructions. A quantitative PHEV N-gene-based RT-PCR (RT-qPCR) developed by Tetracore (Tetracore, Inc., Rockville, MD, USA) and ISU (68 (link)) was used to confirm and quantify PHEV infection in vivo (CDCD pigs) and ex vivo (ALI-PREC cultures). Each RT-qPCR mixture (25-μl final reaction volume) was set up by combining 19 μl of PHEV RT-qPCR master mix and 1 μl of the enzyme blend (reverse transcriptase and RNase inhibitor). An internal control (IC) was used as an extraction control, with 6 μl of the IC added to the lysis buffer. Then, 5 μl of the extracted sample RNA with IC was added to Master Mix. All RT-qPCRs were performed in duplicate, with a negative extraction control (NEC), positive extraction control (PEC), and a “no-template” control (NTC) included in each run. RT-qPCRs were run on a Rotor-Gene Q (Qiagen) under cycling conditions of 48°C for 15 min and 95°C for 2 min for holding and 45 cycles of 95°C for 10 s for denaturation and 60°C for 40 s for amplification. The RT-qPCR results were analyzed using Rotor-Gene Q Pure Detection software (v 2.3.1). Samples with a threshold cycle (CT) above 40 were considered negative.
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5

Extraction of Cell-free and Germline DNA

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To extract cell-free DNA from plasma samples, the QIAamp Circulating Nucleic-Acid Kit (Qiagen) was used according to manufacturer's instructions but the Proteinase K incubation at 60°C was lengthened to 2 hours. All samples were extracted manually using a vacuum manifold (Qiagen). 2-4ml of plasma were used as input. To extract germline DNA from cell pellets, the Qiagen QIAamp DNA Blood Mini Kit (Qiagen) was used according to manufacturer's instructions (spin protocol). 200µl of cell pellet was used as input. For DNA extraction from Formalin-Fixed Paraffin-Embedded (FFPE) lymph node samples 10 µm thick slides were cut. DNA extraction was done with the GeneRead DNA FFPE Kit (Qiagen) according to manufacturer's instructions.
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6

Plasma DNA Extraction Protocol

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Plasma was separated from the blood cells by centrifugation at 2000 g for 10 minutes; the clear plasma phase on top was transferred to a new tube, and centrifuged at 14000 g. The supernatant was transferred to a fresh tube for DNA extraction. DNA was extracted from plasma (5 mL) using the QIAamp Circulating Nucleic Acid (CNA) kit (QIAamp Circulating Nucleic Acid kit, Qiagen, Venlo, Netherlands) according to the manufacturer protocols. Lysis buffer was added to the extension tubes, which were placed directly onto the columns. The columns containing the plasma and lysis buffer were placed on a vacuum manifold (Qiagen), and the liquid was drawn through the column using a vacuum pump (and not centrifuged). The DNA was eluted in a final volume of 50 µL.
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