Reverse Transcription Polymerase Chain Reaction:Article Title: Improved influenza A whole-genome sequencing protocol
Article Snippet: .. Multisegment RT-PCR amplification was performed according to the ONT Ligation Sequencing Influenza A Whole Genome V14 protocol ( ) using the recommended RT-PCR kit (SuperScriptTM III One-Step RT-PCR System with PlatinumTM Taq DNA Polymerase, Invitrogen, USA) and compared to two other RT-PCR kits with alternative RT and DNA polymerases (SuperScriptTM IV One-Step RT-PCR System, Invitrogen, USA and LunaScript ® Multiplex One-Step RT-PCR Kit, New England Biolabs, USA), referred to as SSIII, SSIV, and LS, respectively. ..
Amplification:Article Title: Improved influenza A whole-genome sequencing protocol
Article Snippet: .. Multisegment RT-PCR amplification was performed according to the ONT Ligation Sequencing Influenza A Whole Genome V14 protocol ( ) using the recommended RT-PCR kit (SuperScriptTM III One-Step RT-PCR System with PlatinumTM Taq DNA Polymerase, Invitrogen, USA) and compared to two other RT-PCR kits with alternative RT and DNA polymerases (SuperScriptTM IV One-Step RT-PCR System, Invitrogen, USA and LunaScript ® Multiplex One-Step RT-PCR Kit, New England Biolabs, USA), referred to as SSIII, SSIV, and LS, respectively. ..
Ligation:Article Title: Improved influenza A whole-genome sequencing protocol
Article Snippet: .. Multisegment RT-PCR amplification was performed according to the ONT Ligation Sequencing Influenza A Whole Genome V14 protocol ( ) using the recommended RT-PCR kit (SuperScriptTM III One-Step RT-PCR System with PlatinumTM Taq DNA Polymerase, Invitrogen, USA) and compared to two other RT-PCR kits with alternative RT and DNA polymerases (SuperScriptTM IV One-Step RT-PCR System, Invitrogen, USA and LunaScript ® Multiplex One-Step RT-PCR Kit, New England Biolabs, USA), referred to as SSIII, SSIV, and LS, respectively. ..
Sequencing:Article Title: Improved influenza A whole-genome sequencing protocol
Article Snippet: .. Multisegment RT-PCR amplification was performed according to the ONT Ligation Sequencing Influenza A Whole Genome V14 protocol ( ) using the recommended RT-PCR kit (SuperScriptTM III One-Step RT-PCR System with PlatinumTM Taq DNA Polymerase, Invitrogen, USA) and compared to two other RT-PCR kits with alternative RT and DNA polymerases (SuperScriptTM IV One-Step RT-PCR System, Invitrogen, USA and LunaScript ® Multiplex One-Step RT-PCR Kit, New England Biolabs, USA), referred to as SSIII, SSIV, and LS, respectively. ..
One Step RT-PCR:Article Title: Improved influenza A whole-genome sequencing protocol
Article Snippet: .. Multisegment RT-PCR amplification was performed according to the ONT Ligation Sequencing Influenza A Whole Genome V14 protocol ( ) using the recommended RT-PCR kit (SuperScriptTM III One-Step RT-PCR System with PlatinumTM Taq DNA Polymerase, Invitrogen, USA) and compared to two other RT-PCR kits with alternative RT and DNA polymerases (SuperScriptTM IV One-Step RT-PCR System, Invitrogen, USA and LunaScript ® Multiplex One-Step RT-PCR Kit, New England Biolabs, USA), referred to as SSIII, SSIV, and LS, respectively. ..
Article Title: Isolation of an infectious mammalian chu-like virus from tumor cells of the endangered Tasmanian devil (Sarcophilus harrisii).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Protech C3 Vaccine 25’s Boehringer Ingelheim Cat#9315216501120 Biological samples Tasmanian devils’ tissues and cell lines are described in Tables S1 and S2 Prof. Andrew S. Flies; Prof. Carolyn Hogg N/A Critical commercial assays RNeasy Plus Mini Kit Qiagen Cat# 74136 Illumina Stranded Total RNA Prep with Ribo-Zero plus Illumina Cat# 20040525 SuperScript IV One-Step RT-PCR System ThermoFisher Cat# 12594100 GoTaq RT-qPCR Promega Cat# A6120 HiScribe T7 High Yield RNA Synthesis Kit NEB Cat# E2040S SuperScript IV First-Strand Synthesis System Thermofisher Cat# 18091050 QuantiNova SYBR Green PCR Kit Qiagen Cat# 208052 Deposited data TDCV complete genome GenBank PQ660069 Raw RNA sequences This paper BioProject RJNA1191053 (SRX26888740-SRX26888765) RNA-seq data set Harvey et al.10 SRA (Library ID SRR6380970) Experimental models: Cell lines Tasmanian devil: DFT1 4906 Prof. Andrew S. Flies N/A Tasmanian devil: DFT1 C5065 Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 SN Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 JV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 RV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 TD620 Prof. Andrew S. Flies N/A Tasmanian devil: TD344FBB Prof. Andrew S. Flies N/A Tasmanian devil: TD620 Prof. Andrew S. Flies N/A Mosquitoes: C6/36 ECACC Cat# 89051705 Fish: PLHC-1 ATCC Cat# CRL-2406 Fish: CHSE-214 ECACC Cat# 91041114 Fish: SHK-1 ECACC Cat# 97111106 Fish: OmB ATCC Cat# CRL-3481 Monkey: VeroE6 ECACC Cat# 85020206 Hamster: BHK-21 ECACC Cat# 85011433 Dog: MDCK N/A Prof. Barry Slobedman Oligonucleotides Primer sequences are provided in Table S4 This paper IDT DNA https://sg.idtdna.com/ Software and algorithms Trimmomatic Bolger et al.26 https://github.com/usadellab/Trimmomatic Megahit Li et al.27 https://github.com/voutcn/megahit Diamond Blastx Buchfink et al.28 https://github.com/bbuchfink/diamond Blast + Camacho et al.29 https://conmeehan.github.io/blast+tutorial.html Bowtie2 Langmead and Salzberg30 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Geneious Prime Kearse et al.31 https://www.geneious.com/ Muscle Edgar32 https://www.ebi.ac.uk/jdispatcher/msa/muscle (Continued on next page) ll OPEN ACCESS Current Biology 35, 1–8.e1–e5, July 7, 2025 e1 Report ..
Multiplex Assay:Article Title: Improved influenza A whole-genome sequencing protocol
Article Snippet: .. Multisegment RT-PCR amplification was performed according to the ONT Ligation Sequencing Influenza A Whole Genome V14 protocol ( ) using the recommended RT-PCR kit (SuperScriptTM III One-Step RT-PCR System with PlatinumTM Taq DNA Polymerase, Invitrogen, USA) and compared to two other RT-PCR kits with alternative RT and DNA polymerases (SuperScriptTM IV One-Step RT-PCR System, Invitrogen, USA and LunaScript ® Multiplex One-Step RT-PCR Kit, New England Biolabs, USA), referred to as SSIII, SSIV, and LS, respectively. ..
Virus:Article Title: Isolation of an infectious mammalian chu-like virus from tumor cells of the endangered Tasmanian devil (Sarcophilus harrisii).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Protech C3 Vaccine 25’s Boehringer Ingelheim Cat#9315216501120 Biological samples Tasmanian devils’ tissues and cell lines are described in Tables S1 and S2 Prof. Andrew S. Flies; Prof. Carolyn Hogg N/A Critical commercial assays RNeasy Plus Mini Kit Qiagen Cat# 74136 Illumina Stranded Total RNA Prep with Ribo-Zero plus Illumina Cat# 20040525 SuperScript IV One-Step RT-PCR System ThermoFisher Cat# 12594100 GoTaq RT-qPCR Promega Cat# A6120 HiScribe T7 High Yield RNA Synthesis Kit NEB Cat# E2040S SuperScript IV First-Strand Synthesis System Thermofisher Cat# 18091050 QuantiNova SYBR Green PCR Kit Qiagen Cat# 208052 Deposited data TDCV complete genome GenBank PQ660069 Raw RNA sequences This paper BioProject RJNA1191053 (SRX26888740-SRX26888765) RNA-seq data set Harvey et al.10 SRA (Library ID SRR6380970) Experimental models: Cell lines Tasmanian devil: DFT1 4906 Prof. Andrew S. Flies N/A Tasmanian devil: DFT1 C5065 Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 SN Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 JV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 RV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 TD620 Prof. Andrew S. Flies N/A Tasmanian devil: TD344FBB Prof. Andrew S. Flies N/A Tasmanian devil: TD620 Prof. Andrew S. Flies N/A Mosquitoes: C6/36 ECACC Cat# 89051705 Fish: PLHC-1 ATCC Cat# CRL-2406 Fish: CHSE-214 ECACC Cat# 91041114 Fish: SHK-1 ECACC Cat# 97111106 Fish: OmB ATCC Cat# CRL-3481 Monkey: VeroE6 ECACC Cat# 85020206 Hamster: BHK-21 ECACC Cat# 85011433 Dog: MDCK N/A Prof. Barry Slobedman Oligonucleotides Primer sequences are provided in Table S4 This paper IDT DNA https://sg.idtdna.com/ Software and algorithms Trimmomatic Bolger et al.26 https://github.com/usadellab/Trimmomatic Megahit Li et al.27 https://github.com/voutcn/megahit Diamond Blastx Buchfink et al.28 https://github.com/bbuchfink/diamond Blast + Camacho et al.29 https://conmeehan.github.io/blast+tutorial.html Bowtie2 Langmead and Salzberg30 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Geneious Prime Kearse et al.31 https://www.geneious.com/ Muscle Edgar32 https://www.ebi.ac.uk/jdispatcher/msa/muscle (Continued on next page) ll OPEN ACCESS Current Biology 35, 1–8.e1–e5, July 7, 2025 e1 Report ..
Quantitative RT-PCR:Article Title: Isolation of an infectious mammalian chu-like virus from tumor cells of the endangered Tasmanian devil (Sarcophilus harrisii).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Protech C3 Vaccine 25’s Boehringer Ingelheim Cat#9315216501120 Biological samples Tasmanian devils’ tissues and cell lines are described in Tables S1 and S2 Prof. Andrew S. Flies; Prof. Carolyn Hogg N/A Critical commercial assays RNeasy Plus Mini Kit Qiagen Cat# 74136 Illumina Stranded Total RNA Prep with Ribo-Zero plus Illumina Cat# 20040525 SuperScript IV One-Step RT-PCR System ThermoFisher Cat# 12594100 GoTaq RT-qPCR Promega Cat# A6120 HiScribe T7 High Yield RNA Synthesis Kit NEB Cat# E2040S SuperScript IV First-Strand Synthesis System Thermofisher Cat# 18091050 QuantiNova SYBR Green PCR Kit Qiagen Cat# 208052 Deposited data TDCV complete genome GenBank PQ660069 Raw RNA sequences This paper BioProject RJNA1191053 (SRX26888740-SRX26888765) RNA-seq data set Harvey et al.10 SRA (Library ID SRR6380970) Experimental models: Cell lines Tasmanian devil: DFT1 4906 Prof. Andrew S. Flies N/A Tasmanian devil: DFT1 C5065 Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 SN Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 JV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 RV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 TD620 Prof. Andrew S. Flies N/A Tasmanian devil: TD344FBB Prof. Andrew S. Flies N/A Tasmanian devil: TD620 Prof. Andrew S. Flies N/A Mosquitoes: C6/36 ECACC Cat# 89051705 Fish: PLHC-1 ATCC Cat# CRL-2406 Fish: CHSE-214 ECACC Cat# 91041114 Fish: SHK-1 ECACC Cat# 97111106 Fish: OmB ATCC Cat# CRL-3481 Monkey: VeroE6 ECACC Cat# 85020206 Hamster: BHK-21 ECACC Cat# 85011433 Dog: MDCK N/A Prof. Barry Slobedman Oligonucleotides Primer sequences are provided in Table S4 This paper IDT DNA https://sg.idtdna.com/ Software and algorithms Trimmomatic Bolger et al.26 https://github.com/usadellab/Trimmomatic Megahit Li et al.27 https://github.com/voutcn/megahit Diamond Blastx Buchfink et al.28 https://github.com/bbuchfink/diamond Blast + Camacho et al.29 https://conmeehan.github.io/blast+tutorial.html Bowtie2 Langmead and Salzberg30 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Geneious Prime Kearse et al.31 https://www.geneious.com/ Muscle Edgar32 https://www.ebi.ac.uk/jdispatcher/msa/muscle (Continued on next page) ll OPEN ACCESS Current Biology 35, 1–8.e1–e5, July 7, 2025 e1 Report ..
SYBR Green Assay:Article Title: Isolation of an infectious mammalian chu-like virus from tumor cells of the endangered Tasmanian devil (Sarcophilus harrisii).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Protech C3 Vaccine 25’s Boehringer Ingelheim Cat#9315216501120 Biological samples Tasmanian devils’ tissues and cell lines are described in Tables S1 and S2 Prof. Andrew S. Flies; Prof. Carolyn Hogg N/A Critical commercial assays RNeasy Plus Mini Kit Qiagen Cat# 74136 Illumina Stranded Total RNA Prep with Ribo-Zero plus Illumina Cat# 20040525 SuperScript IV One-Step RT-PCR System ThermoFisher Cat# 12594100 GoTaq RT-qPCR Promega Cat# A6120 HiScribe T7 High Yield RNA Synthesis Kit NEB Cat# E2040S SuperScript IV First-Strand Synthesis System Thermofisher Cat# 18091050 QuantiNova SYBR Green PCR Kit Qiagen Cat# 208052 Deposited data TDCV complete genome GenBank PQ660069 Raw RNA sequences This paper BioProject RJNA1191053 (SRX26888740-SRX26888765) RNA-seq data set Harvey et al.10 SRA (Library ID SRR6380970) Experimental models: Cell lines Tasmanian devil: DFT1 4906 Prof. Andrew S. Flies N/A Tasmanian devil: DFT1 C5065 Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 SN Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 JV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 RV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 TD620 Prof. Andrew S. Flies N/A Tasmanian devil: TD344FBB Prof. Andrew S. Flies N/A Tasmanian devil: TD620 Prof. Andrew S. Flies N/A Mosquitoes: C6/36 ECACC Cat# 89051705 Fish: PLHC-1 ATCC Cat# CRL-2406 Fish: CHSE-214 ECACC Cat# 91041114 Fish: SHK-1 ECACC Cat# 97111106 Fish: OmB ATCC Cat# CRL-3481 Monkey: VeroE6 ECACC Cat# 85020206 Hamster: BHK-21 ECACC Cat# 85011433 Dog: MDCK N/A Prof. Barry Slobedman Oligonucleotides Primer sequences are provided in Table S4 This paper IDT DNA https://sg.idtdna.com/ Software and algorithms Trimmomatic Bolger et al.26 https://github.com/usadellab/Trimmomatic Megahit Li et al.27 https://github.com/voutcn/megahit Diamond Blastx Buchfink et al.28 https://github.com/bbuchfink/diamond Blast + Camacho et al.29 https://conmeehan.github.io/blast+tutorial.html Bowtie2 Langmead and Salzberg30 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Geneious Prime Kearse et al.31 https://www.geneious.com/ Muscle Edgar32 https://www.ebi.ac.uk/jdispatcher/msa/muscle (Continued on next page) ll OPEN ACCESS Current Biology 35, 1–8.e1–e5, July 7, 2025 e1 Report ..
Polymerase Chain Reaction:Article Title: Isolation of an infectious mammalian chu-like virus from tumor cells of the endangered Tasmanian devil (Sarcophilus harrisii).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Protech C3 Vaccine 25’s Boehringer Ingelheim Cat#9315216501120 Biological samples Tasmanian devils’ tissues and cell lines are described in Tables S1 and S2 Prof. Andrew S. Flies; Prof. Carolyn Hogg N/A Critical commercial assays RNeasy Plus Mini Kit Qiagen Cat# 74136 Illumina Stranded Total RNA Prep with Ribo-Zero plus Illumina Cat# 20040525 SuperScript IV One-Step RT-PCR System ThermoFisher Cat# 12594100 GoTaq RT-qPCR Promega Cat# A6120 HiScribe T7 High Yield RNA Synthesis Kit NEB Cat# E2040S SuperScript IV First-Strand Synthesis System Thermofisher Cat# 18091050 QuantiNova SYBR Green PCR Kit Qiagen Cat# 208052 Deposited data TDCV complete genome GenBank PQ660069 Raw RNA sequences This paper BioProject RJNA1191053 (SRX26888740-SRX26888765) RNA-seq data set Harvey et al.10 SRA (Library ID SRR6380970) Experimental models: Cell lines Tasmanian devil: DFT1 4906 Prof. Andrew S. Flies N/A Tasmanian devil: DFT1 C5065 Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 SN Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 JV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 RV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 TD620 Prof. Andrew S. Flies N/A Tasmanian devil: TD344FBB Prof. Andrew S. Flies N/A Tasmanian devil: TD620 Prof. Andrew S. Flies N/A Mosquitoes: C6/36 ECACC Cat# 89051705 Fish: PLHC-1 ATCC Cat# CRL-2406 Fish: CHSE-214 ECACC Cat# 91041114 Fish: SHK-1 ECACC Cat# 97111106 Fish: OmB ATCC Cat# CRL-3481 Monkey: VeroE6 ECACC Cat# 85020206 Hamster: BHK-21 ECACC Cat# 85011433 Dog: MDCK N/A Prof. Barry Slobedman Oligonucleotides Primer sequences are provided in Table S4 This paper IDT DNA https://sg.idtdna.com/ Software and algorithms Trimmomatic Bolger et al.26 https://github.com/usadellab/Trimmomatic Megahit Li et al.27 https://github.com/voutcn/megahit Diamond Blastx Buchfink et al.28 https://github.com/bbuchfink/diamond Blast + Camacho et al.29 https://conmeehan.github.io/blast+tutorial.html Bowtie2 Langmead and Salzberg30 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Geneious Prime Kearse et al.31 https://www.geneious.com/ Muscle Edgar32 https://www.ebi.ac.uk/jdispatcher/msa/muscle (Continued on next page) ll OPEN ACCESS Current Biology 35, 1–8.e1–e5, July 7, 2025 e1 Report ..
RNA Sequencing:Article Title: Isolation of an infectious mammalian chu-like virus from tumor cells of the endangered Tasmanian devil (Sarcophilus harrisii).
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Protech C3 Vaccine 25’s Boehringer Ingelheim Cat#9315216501120 Biological samples Tasmanian devils’ tissues and cell lines are described in Tables S1 and S2 Prof. Andrew S. Flies; Prof. Carolyn Hogg N/A Critical commercial assays RNeasy Plus Mini Kit Qiagen Cat# 74136 Illumina Stranded Total RNA Prep with Ribo-Zero plus Illumina Cat# 20040525 SuperScript IV One-Step RT-PCR System ThermoFisher Cat# 12594100 GoTaq RT-qPCR Promega Cat# A6120 HiScribe T7 High Yield RNA Synthesis Kit NEB Cat# E2040S SuperScript IV First-Strand Synthesis System Thermofisher Cat# 18091050 QuantiNova SYBR Green PCR Kit Qiagen Cat# 208052 Deposited data TDCV complete genome GenBank PQ660069 Raw RNA sequences This paper BioProject RJNA1191053 (SRX26888740-SRX26888765) RNA-seq data set Harvey et al.10 SRA (Library ID SRR6380970) Experimental models: Cell lines Tasmanian devil: DFT1 4906 Prof. Andrew S. Flies N/A Tasmanian devil: DFT1 C5065 Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 SN Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 JV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 RV Prof. Andrew S. Flies N/A Tasmanian devil: DFT2 TD620 Prof. Andrew S. Flies N/A Tasmanian devil: TD344FBB Prof. Andrew S. Flies N/A Tasmanian devil: TD620 Prof. Andrew S. Flies N/A Mosquitoes: C6/36 ECACC Cat# 89051705 Fish: PLHC-1 ATCC Cat# CRL-2406 Fish: CHSE-214 ECACC Cat# 91041114 Fish: SHK-1 ECACC Cat# 97111106 Fish: OmB ATCC Cat# CRL-3481 Monkey: VeroE6 ECACC Cat# 85020206 Hamster: BHK-21 ECACC Cat# 85011433 Dog: MDCK N/A Prof. Barry Slobedman Oligonucleotides Primer sequences are provided in Table S4 This paper IDT DNA https://sg.idtdna.com/ Software and algorithms Trimmomatic Bolger et al.26 https://github.com/usadellab/Trimmomatic Megahit Li et al.27 https://github.com/voutcn/megahit Diamond Blastx Buchfink et al.28 https://github.com/bbuchfink/diamond Blast + Camacho et al.29 https://conmeehan.github.io/blast+tutorial.html Bowtie2 Langmead and Salzberg30 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Geneious Prime Kearse et al.31 https://www.geneious.com/ Muscle Edgar32 https://www.ebi.ac.uk/jdispatcher/msa/muscle (Continued on next page) ll OPEN ACCESS Current Biology 35, 1–8.e1–e5, July 7, 2025 e1 Report ..
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