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4 protocols using sequenase 2

1

Microdissection and Amplification of Sex Chromosomes

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Microdissection of sex chromosomes was performed according to described protocol [27 (link)] with some modifications. For each DNA probe, 15–20 copies of the chromosome or chromosome region were collected by extended glass needle using a micromanipulator MR (Zeiss, Oberkochen, Germany). Proteinase K treatment and low temperature cycles of degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) with Sequenase 2.0 (ThermoFisher Scientific, Waltham, MA, USA) were performed exactly as described [27 (link)]. High temperature cycles of DNA amplification were carried out with Encyclo Polymerase mix (Evrogen, Moscow, Russia) in 33 cycles of PCR according to the producer’s recommendation. DNA probes were labeled in an additional 25 cycles of PCR with Tamra-5-dUTP and Fluorescein-12-dUTP (Biosan, Novosibirsk, Russia) as described [28 (link)].
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2

HPIV3 Genome Consensus Assembly Protocols

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Reference-guided genome consensus assemblies were generated for each sample by aligning the sequencing reads to HPIV3 strain 14072 (GenBank accession no. EU424062.1) using BWA-MEM v0.7.5a-r405, removing multimapped reads, and resolving conflicts using a majority rule. (Priority was given in the order A > C > G > T in the event of a tie.) Sequence coverage was determined using the SAMtools depth tool v1.1 (29 (link)). mNGS libraries for day 28 lung organoids and day 14 CV1 passage experiments were prepared as described previously (30 (link)). RNA was extracted from viral supernatant using the Zymo Viral RNA kit and treated with Turbo DNase I at 37°C for 20 min (Thermo Fisher). RNA was reverse transcribed using random hexamers SuperScript IV (Thermo Fisher), and double-stranded cDNA was produced using the same random hexamers with Sequenase 2.0 (Thermo Fisher) and cleaned using a Zymo DNA Clean and Concentrator. Sequencing libraries were generated using one-third volumes of Nextera XT tagmentation followed by 20 cycles of dual-indexed PCR and a 0.8X Ampure bead cleanup (Beckman Coulter). Libraries were sequenced on an Illumina MiSeq. Sequencing reads are deposited in NCBI under BioProject PRJNA524147.
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3

Complete Genome Sequencing of Hendra Virus

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We subjected samples positive for HeV-var by paramyxovirus RT-PCR to meta-transcriptomic sequencing to determine the complete genome sequence and identify any co-infecting agents. RNA was reverse transcribed with Invitrogen SSIV VILO Master Mix (ThermoFisher) and FastSelect reagent (QIAGEN). We performed second-strand synthesis with Sequenase 2.0 (ThermoFisher) before DNA library preparation with Nextera XT (Illumina) and unique dual indexes. We performed sequencing on an Illumina NextSeq system to generate 100 million paired reads (75 bp) per library.
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4

Microdissection and Labeling of Pericentromeric DNA

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DNA-probe from the pericentromeric region (PCPAflaCEN) of the largest autosome of A. flavicollis specimen #1851 was generated by metaphase chromosome microdissection followed by a degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) with Sequenase 2.0 (ThermoFisher Scientific, Waltham, MA, USA) according to standard protocol [39 (link),45 ,46 (link)]. Briefly, the chromosome stained with Giemsa (Sigma-Aldrich, Saint Louis, MO, USA) was dissected with an extended glass needle controlled with micromanipulator MR (ZEISS, Jena, Germany) ) on an inverted microscope AXIOWERT10; one copy of the pericentromeric region of the largest autosome was transferred into the extended and siliconized tip of Pasteur pipet with 40 nL collection solution, containing 30% glycerol, 10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 0.1% SDS, 0.1% Triton X-100, 500 μg/mL proteinase K (Boehringer Mannheim, Indianapolis, IN, USA). Dissected material was treated for two hours in a moist chamber at 60 °C and then transferred into 5 µL of PCR mixture for DOP-PCR, which was performed as described [46 (link),47 (link)]. DNA labeling was carried out with 20 additional cycles of PCR performed with an additional fluorescent labeled nucleotide Alexa Fluor 488-5-dUTP (Invitrogen, Waltham, MA, USA) [46 (link),48 (link)].
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