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4 protocols using dynabeads myone carboxylic acid beads

1

Single-Cell Lysis and Reverse Transcription

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After digestion, single cells were placed into 5‐μL cell lysis buffer by mouth pipetting. The cell lysis buffer contained 0.2 μL balanced Dynabeads™ MyOne™ Carboxylic Acid beads (Thermo Fisher Scientific, Cat. 65011), 0.8 U/μL RNase Inhibitor (Takara, Cat. 2313B), 0.2% Triton X‐100 (Sigma‐Aldrich, Cat. X100), 2 μL 5X SuperScript II first‐strand buffer (Invitrogen), 0.4 μM reverse transcription (RT) primer (AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTT), 10 nM DTT and 0.04% Tween‐20. The single‐cell suspension was vortexed thoroughly for 30 s and placed on an ice‐cold magnet rack.
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2

DNA Sequencing Library Preparation

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DNA was quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). 250 ng DNA was sheared in the Covaris® S2 instrument (Covaris, Inc.) to an insert size of approximately 650 bp. Fifty nanograms of sheared DNA was used for preparation of sequencing libraries with the ThruPLEX® DNA-seq Kit (Rubicon Genomics) according to the manufacturer’s instructions using provided primers with ten cycles for amplification. Primer sequences were as follows: 5’: AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT with NNNNNNNN being a TruSeq HT i5 index and 3’: GTTCGTCTTCTGCCGTATGCTCTANNNNNNNNCACTGACCTCAAGTCTGCACACGAGAAGGCTAGA with NNNNNNNN being a TruSeq HT i7 index.
PCR products were purified on the MBS Magnatrix 1200 automated workstation (NorDiag) with Dynabeads® MyOne carboxylic acid beads (Thermo Fisher Scientific). Purity of the samples and insert size distribution were inspected using the High Sensitivity DNA Kit on the Agilent 2100 Bioanalyzer instrument (Agilent Technologies). DNA libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and equimolar concentrations of 12 samples were pooled and further purified using Agencourt AMPure XP (Beckman Coulter, Inc.). Library pools with a final concentration of 10 nM DNA were submitted to one flow cell per pool and sequenced using the MiSeq V3 chemistry (Illumina).
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3

Recombinant RBD Protein Immobilization

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Recombinantly-expressed RBD was covalently loaded onto Dynabeads® MyOne Carboxylic Acid beads (Thermo 65011, Thermo 65012) according to the manufacturer-provided protocol for “Two-Step Coating Procedure using NHS”. In brief, for a single preparation, 1.5 mL of bead suspension was dispensed and washed twice with 1.5 mL of 25 mM MES, pH 6.0 for 10 min. at room temperature. Following washes, bead chemistry was activated by suspending the beads into 1.5 mL of freshly-prepared 50 mg/mL N-Hydroxysuccinimide (NHS), mixing in 1.5 mL of freshly-prepared 50 mg/mL 1-Ethyl-3-(3dimethylaminopropyl) carbodiimide (EDC), and incubating for 30 min. at room temperature. Following activation, the beads were again washed twice with 1.5 mL of 25 mM MES, pH 6.0 for 10 min. at room temperature. Activated beads were suspended into 1 mL 25 mM MES, pH 6.0 to which 1.5 mg of RBD protein was added. The sample was mixed and incubated for 30 min. at room temperature. Next, the beads were pulled down, the supernatant was discarded, and loading was quenched by incubating the beads in 1 mL of 50 mM Tris, pH 6.8, for 15 min. at room temperature. After quenching, beads were washed four times in 1 mL 1x PBS + 0.1% human serum albumin (HSA), and finally suspended into 3 mL 1x PBS + 0.1% HSA for storage at 4°C.
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4

Vitamin D Binding Protein Assay

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Dynabeads MyOne™ carboxylic acid beads, EZLink™ Sulfo-NHS-LC-Biotinylation Kit, succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC), and 4′-hydroxyazobenzene-2-carboxylic acid (HABA) solution are obtained from Thermo Fisher; perfluorohexanoate(PFHxA), methanol, EDC, and NHS are purchased from Sigma; an AKTA purifier is purchased from GE healthcare; biotinylated vitamin D (BVD) is obtained from DIASource; HRP is purchased from BBI solutions; streptavidin is purchased from NeuroPeptide from China; a microscope is purchased from Olympus; an automicroplate chemiluminescent analyzer is supplied by Baiming Biotechnology from China; and an automagnetic beads chemiluminescent analyzer is supplied by Zecheng Biotechnology from China. Mice used for antibody production are obtained from Jiangnan University; VD is purchased from Conju-Probe.
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