Reverse Transcription Polymerase Chain Reaction:Article Title: Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data
Article Snippet: .. The primary RBD RT-PCR was performed using the Superscript IV One-Step RT-PCR System (ThermoFisher Scientific,12594100, Waltham, MA, USA). .. Primary RT-PCR amplification was performed as follows: [25°C (2:00) + 50°C (20:00) + 95°C (2:00)] + ([95°C (0:15) + 55°C (0:30) + 72°C (1:00)] × 25) cycles using the MiSeq primary PCR primers 5’-CAAACTTCTAACTTTAGAGTCCAACC-3’ and 5’-AAGTCCACAAACAGTTGCT-3’, and an additional reaction was conducted to exclude Omicron lineages using the primer sets 5’-CCCTGATAAAGAACAGCAACC-3’ and 5’-TATATAATTCCGCATCATTTTCCAC-3’.
Article Title: APOBEC3A deaminase catalyzes site-specific editing of transfer RNAs
Article Snippet: .. Products of the deamination reaction were purified using MinElute PCR Purification kit (Qiagen), followed by one-step reverse transcription-polymerase chain reaction (RT-PCR) using SuperScript IV One-Step RT-PCR System (ThermoFisher Scientific) according to the manufacturer’s protocol. .. RT-PCR products were cloned into pCR Blunt II-TOPO vector (ThermoFisher Scientific).
Article Title: Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data.
Article Snippet: .. Amplifying the ohio cryptic lineage The primary RBD RT-PCR was performed using the Superscript IV One-Step RT-PCR System (ThermoFisher Scientific,12594100, Waltham, MA, USA). .. Primary RT-PCR amplification was performed as follows: [25°C (2:00) + 50°C (20:00) + 95°C (2:00)] + ([95°C (0:15) + 55°C (0:30) + 72°C (1:00)] × 25) cycles using the MiSeq primary PCR primers 5’-CAAACTTCTAACTTTAGAGTCCAACC-3’ and 5’-AAGTCCACAAACAGTTGCT-3’, and an additional reaction was conducted to exclude Omicron lineages using the primer sets 5’-CCCTGATAAAGAACAGCAACC-3’ and 5’-TATATAATTC CGCATCATTTTCCAC-3’.
One Step RT-PCR:Article Title: Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data
Article Snippet: .. The primary RBD RT-PCR was performed using the Superscript IV One-Step RT-PCR System (ThermoFisher Scientific,12594100, Waltham, MA, USA). .. Primary RT-PCR amplification was performed as follows: [25°C (2:00) + 50°C (20:00) + 95°C (2:00)] + ([95°C (0:15) + 55°C (0:30) + 72°C (1:00)] × 25) cycles using the MiSeq primary PCR primers 5’-CAAACTTCTAACTTTAGAGTCCAACC-3’ and 5’-AAGTCCACAAACAGTTGCT-3’, and an additional reaction was conducted to exclude Omicron lineages using the primer sets 5’-CCCTGATAAAGAACAGCAACC-3’ and 5’-TATATAATTCCGCATCATTTTCCAC-3’.
Article Title: APOBEC3A deaminase catalyzes site-specific editing of transfer RNAs
Article Snippet: .. Products of the deamination reaction were purified using MinElute PCR Purification kit (Qiagen), followed by one-step reverse transcription-polymerase chain reaction (RT-PCR) using SuperScript IV One-Step RT-PCR System (ThermoFisher Scientific) according to the manufacturer’s protocol. .. RT-PCR products were cloned into pCR Blunt II-TOPO vector (ThermoFisher Scientific).
Article Title: Efficacy of baloxavir marboxil against bovine H5N1 virus in mice
Article Snippet: Viral RNA was extracted by using a QIAamp Viral RNA Mini Kit (QIAGEN). .. The All eight viral RNA segments of influenza A virus were simultaneously amplified by using the SuperScript IV one-step RT-PCR system (Thermo Fisher Scientific) with universal primers [MBTuni-12-R (5′-ACG CGT GAT CAG CRA AAG CAG G-3′) and MBTuni-13 (5′-ACG CGT GAT CAG TAG AAA CAA GG-3′)] targeting the highly conserved sequence of the viral RNA termini . .. The multisegment RT-PCR (M-RTPCR) products were processed for sequencing libraries by using a QIAseq FX DNA Library Kit (QIAGEN) and were then analyzed by using the iSeq 100 System (Illumina) with a iSeq 100 i1 Reagent v2 (300-cycle) or the MiSeq i100 plus system (Illumina) with MiSeq i100 Series 25 M Reagent Kit (300 cycles).
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 ..
Article Title: Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data.
Article Snippet: .. Amplifying the ohio cryptic lineage The primary RBD RT-PCR was performed using the Superscript IV One-Step RT-PCR System (ThermoFisher Scientific,12594100, Waltham, MA, USA). .. Primary RT-PCR amplification was performed as follows: [25°C (2:00) + 50°C (20:00) + 95°C (2:00)] + ([95°C (0:15) + 55°C (0:30) + 72°C (1:00)] × 25) cycles using the MiSeq primary PCR primers 5’-CAAACTTCTAACTTTAGAGTCCAACC-3’ and 5’-AAGTCCACAAACAGTTGCT-3’, and an additional reaction was conducted to exclude Omicron lineages using the primer sets 5’-CCCTGATAAAGAACAGCAACC-3’ and 5’-TATATAATTC CGCATCATTTTCCAC-3’.
Article Title: Efficacy of baloxavir marboxil against bovine H5N1 virus in mice.
Article Snippet: Viral RNA was extracted by using a QIAamp Viral RNA Mini Kit (QIAGEN). .. The All eight viral RNA segments of influenza A virus were simultaneously amplified by using the SuperScript IV one-step RT-PCR system (Thermo Fisher Scientific) with universal primers [MBTuni-12-R (5′-ACGCGTGATCAGCRAAAGCAGG-3′) andMBTuni-13 (5′-ACGCGT GAT CAG TAG AAA CAA GG-3′)] targeting the highly conserved sequence of the viral RNA termini13. .. The multisegment RT-PCR (MRTPCR) products were processed for sequencing libraries by using a QIAseq FX DNA Library Kit (QIAGEN) and were then analyzed by using the iSeq 100 System (Illumina) with a iSeq 100 i1 Reagent v2 (300- cycle) or the MiSeq i100 plus system (Illumina) with MiSeq i100 Series 25M Reagent Kit (300 cycles).
Purification:Article Title: APOBEC3A deaminase catalyzes site-specific editing of transfer RNAs
Article Snippet: .. Products of the deamination reaction were purified using MinElute PCR Purification kit (Qiagen), followed by one-step reverse transcription-polymerase chain reaction (RT-PCR) using SuperScript IV One-Step RT-PCR System (ThermoFisher Scientific) according to the manufacturer’s protocol. .. RT-PCR products were cloned into pCR Blunt II-TOPO vector (ThermoFisher Scientific).
Polymerase Chain Reaction:Article Title: APOBEC3A deaminase catalyzes site-specific editing of transfer RNAs
Article Snippet: .. Products of the deamination reaction were purified using MinElute PCR Purification kit (Qiagen), followed by one-step reverse transcription-polymerase chain reaction (RT-PCR) using SuperScript IV One-Step RT-PCR System (ThermoFisher Scientific) according to the manufacturer’s protocol. .. RT-PCR products were cloned into pCR Blunt II-TOPO vector (ThermoFisher Scientific).
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 ..
Virus:Article Title: Efficacy of baloxavir marboxil against bovine H5N1 virus in mice
Article Snippet: Viral RNA was extracted by using a QIAamp Viral RNA Mini Kit (QIAGEN). .. The All eight viral RNA segments of influenza A virus were simultaneously amplified by using the SuperScript IV one-step RT-PCR system (Thermo Fisher Scientific) with universal primers [MBTuni-12-R (5′-ACG CGT GAT CAG CRA AAG CAG G-3′) and MBTuni-13 (5′-ACG CGT GAT CAG TAG AAA CAA GG-3′)] targeting the highly conserved sequence of the viral RNA termini . .. The multisegment RT-PCR (M-RTPCR) products were processed for sequencing libraries by using a QIAseq FX DNA Library Kit (QIAGEN) and were then analyzed by using the iSeq 100 System (Illumina) with a iSeq 100 i1 Reagent v2 (300-cycle) or the MiSeq i100 plus system (Illumina) with MiSeq i100 Series 25 M Reagent Kit (300 cycles).
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 ..
Article Title: Efficacy of baloxavir marboxil against bovine H5N1 virus in mice.
Article Snippet: Viral RNA was extracted by using a QIAamp Viral RNA Mini Kit (QIAGEN). .. The All eight viral RNA segments of influenza A virus were simultaneously amplified by using the SuperScript IV one-step RT-PCR system (Thermo Fisher Scientific) with universal primers [MBTuni-12-R (5′-ACGCGTGATCAGCRAAAGCAGG-3′) andMBTuni-13 (5′-ACGCGT GAT CAG TAG AAA CAA GG-3′)] targeting the highly conserved sequence of the viral RNA termini13. .. The multisegment RT-PCR (MRTPCR) products were processed for sequencing libraries by using a QIAseq FX DNA Library Kit (QIAGEN) and were then analyzed by using the iSeq 100 System (Illumina) with a iSeq 100 i1 Reagent v2 (300- cycle) or the MiSeq i100 plus system (Illumina) with MiSeq i100 Series 25M Reagent Kit (300 cycles).
Amplification:Article Title: Efficacy of baloxavir marboxil against bovine H5N1 virus in mice
Article Snippet: Viral RNA was extracted by using a QIAamp Viral RNA Mini Kit (QIAGEN). .. The All eight viral RNA segments of influenza A virus were simultaneously amplified by using the SuperScript IV one-step RT-PCR system (Thermo Fisher Scientific) with universal primers [MBTuni-12-R (5′-ACG CGT GAT CAG CRA AAG CAG G-3′) and MBTuni-13 (5′-ACG CGT GAT CAG TAG AAA CAA GG-3′)] targeting the highly conserved sequence of the viral RNA termini . .. The multisegment RT-PCR (M-RTPCR) products were processed for sequencing libraries by using a QIAseq FX DNA Library Kit (QIAGEN) and were then analyzed by using the iSeq 100 System (Illumina) with a iSeq 100 i1 Reagent v2 (300-cycle) or the MiSeq i100 plus system (Illumina) with MiSeq i100 Series 25 M Reagent Kit (300 cycles).
Article Title: Efficacy of baloxavir marboxil against bovine H5N1 virus in mice.
Article Snippet: Viral RNA was extracted by using a QIAamp Viral RNA Mini Kit (QIAGEN). .. The All eight viral RNA segments of influenza A virus were simultaneously amplified by using the SuperScript IV one-step RT-PCR system (Thermo Fisher Scientific) with universal primers [MBTuni-12-R (5′-ACGCGTGATCAGCRAAAGCAGG-3′) andMBTuni-13 (5′-ACGCGT GAT CAG TAG AAA CAA GG-3′)] targeting the highly conserved sequence of the viral RNA termini13. .. The multisegment RT-PCR (MRTPCR) products were processed for sequencing libraries by using a QIAseq FX DNA Library Kit (QIAGEN) and were then analyzed by using the iSeq 100 System (Illumina) with a iSeq 100 i1 Reagent v2 (300- cycle) or the MiSeq i100 plus system (Illumina) with MiSeq i100 Series 25M Reagent Kit (300 cycles).
Sequencing:Article Title: Efficacy of baloxavir marboxil against bovine H5N1 virus in mice
Article Snippet: Viral RNA was extracted by using a QIAamp Viral RNA Mini Kit (QIAGEN). .. The All eight viral RNA segments of influenza A virus were simultaneously amplified by using the SuperScript IV one-step RT-PCR system (Thermo Fisher Scientific) with universal primers [MBTuni-12-R (5′-ACG CGT GAT CAG CRA AAG CAG G-3′) and MBTuni-13 (5′-ACG CGT GAT CAG TAG AAA CAA GG-3′)] targeting the highly conserved sequence of the viral RNA termini . .. The multisegment RT-PCR (M-RTPCR) products were processed for sequencing libraries by using a QIAseq FX DNA Library Kit (QIAGEN) and were then analyzed by using the iSeq 100 System (Illumina) with a iSeq 100 i1 Reagent v2 (300-cycle) or the MiSeq i100 plus system (Illumina) with MiSeq i100 Series 25 M Reagent Kit (300 cycles).
Article Title: Efficacy of baloxavir marboxil against bovine H5N1 virus in mice.
Article Snippet: Viral RNA was extracted by using a QIAamp Viral RNA Mini Kit (QIAGEN). .. The All eight viral RNA segments of influenza A virus were simultaneously amplified by using the SuperScript IV one-step RT-PCR system (Thermo Fisher Scientific) with universal primers [MBTuni-12-R (5′-ACGCGTGATCAGCRAAAGCAGG-3′) andMBTuni-13 (5′-ACGCGT GAT CAG TAG AAA CAA GG-3′)] targeting the highly conserved sequence of the viral RNA termini13. .. The multisegment RT-PCR (MRTPCR) products were processed for sequencing libraries by using a QIAseq FX DNA Library Kit (QIAGEN) and were then analyzed by using the iSeq 100 System (Illumina) with a iSeq 100 i1 Reagent v2 (300- cycle) or the MiSeq i100 plus system (Illumina) with MiSeq i100 Series 25M Reagent Kit (300 cycles).
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 ..
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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