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mfei hf  (New England Biolabs)
94
New England Biolabs mfei hf
Rational design and the experimental validation of the LIS-seq workflow (A) Schematic representation of the experimental strategy of the establishment of single provirus-integrated cellular clones (sinpro clones). A total of 14 clones, in which proviruses demonstrated different transcriptional phenotypes were assigned to four different groups, including the active group (the A group, 4 clones), the attenuated active group (the A-group, 6 clones), the silent group (the S group, 3 clones) and the fluctuation group (the F group, 1 clone) and applied to LIS-seq for the identification of HIV integration sites. (B) Schematic representation of the experimental workflow of LIS-seq. Genomic DNA isolated from sinpro clones was digested with restriction enzymes, HpyCH4III and BplI, followed by in vitro transcription, and RT-PCR amplification with primers embedded with Illumina adaptor sequences. Amplicons are sequenced as 50 bp single reads on a NovaSeq 6000 sequencer (Illumina). (C) Verification of restriction enzyme digestion of genomic DNA isolated from sinpro clones. Genomic DNA is either subjected to BplI plus HpyCH4III (lane 1) or BplI plus HpyCH4III as well <t>as</t> <t>MfeI-HF</t> plus Hpy166I (lane 2). Of note, genomic DNA is digested independently by both pairs of restriction enzymes shown in lane 2. (D) Verification of the production of single-stranded RNA (ssRNA) resulting from in vitro transcription. ssRNA was used as the template for the performance of RT-PCR amplification, yielding a correct 220 bp product. (E) Expected result from the sequencing amplicon using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus in 14 sinpro clones. (F) Expected result from the sequencing amplicon in a pool of infected cells using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus.
Mfei Hf, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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r3589s  (New England Biolabs)
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New England Biolabs r3589s
Rational design and the experimental validation of the LIS-seq workflow (A) Schematic representation of the experimental strategy of the establishment of single provirus-integrated cellular clones (sinpro clones). A total of 14 clones, in which proviruses demonstrated different transcriptional phenotypes were assigned to four different groups, including the active group (the A group, 4 clones), the attenuated active group (the A-group, 6 clones), the silent group (the S group, 3 clones) and the fluctuation group (the F group, 1 clone) and applied to LIS-seq for the identification of HIV integration sites. (B) Schematic representation of the experimental workflow of LIS-seq. Genomic DNA isolated from sinpro clones was digested with restriction enzymes, HpyCH4III and BplI, followed by in vitro transcription, and RT-PCR amplification with primers embedded with Illumina adaptor sequences. Amplicons are sequenced as 50 bp single reads on a NovaSeq 6000 sequencer (Illumina). (C) Verification of restriction enzyme digestion of genomic DNA isolated from sinpro clones. Genomic DNA is either subjected to BplI plus HpyCH4III (lane 1) or BplI plus HpyCH4III as well <t>as</t> <t>MfeI-HF</t> plus Hpy166I (lane 2). Of note, genomic DNA is digested independently by both pairs of restriction enzymes shown in lane 2. (D) Verification of the production of single-stranded RNA (ssRNA) resulting from in vitro transcription. ssRNA was used as the template for the performance of RT-PCR amplification, yielding a correct 220 bp product. (E) Expected result from the sequencing amplicon using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus in 14 sinpro clones. (F) Expected result from the sequencing amplicon in a pool of infected cells using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus.
R3589s, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mfei xmai  (New England Biolabs)
96
New England Biolabs mfei xmai
Rational design and the experimental validation of the LIS-seq workflow (A) Schematic representation of the experimental strategy of the establishment of single provirus-integrated cellular clones (sinpro clones). A total of 14 clones, in which proviruses demonstrated different transcriptional phenotypes were assigned to four different groups, including the active group (the A group, 4 clones), the attenuated active group (the A-group, 6 clones), the silent group (the S group, 3 clones) and the fluctuation group (the F group, 1 clone) and applied to LIS-seq for the identification of HIV integration sites. (B) Schematic representation of the experimental workflow of LIS-seq. Genomic DNA isolated from sinpro clones was digested with restriction enzymes, HpyCH4III and BplI, followed by in vitro transcription, and RT-PCR amplification with primers embedded with Illumina adaptor sequences. Amplicons are sequenced as 50 bp single reads on a NovaSeq 6000 sequencer (Illumina). (C) Verification of restriction enzyme digestion of genomic DNA isolated from sinpro clones. Genomic DNA is either subjected to BplI plus HpyCH4III (lane 1) or BplI plus HpyCH4III as well <t>as</t> <t>MfeI-HF</t> plus Hpy166I (lane 2). Of note, genomic DNA is digested independently by both pairs of restriction enzymes shown in lane 2. (D) Verification of the production of single-stranded RNA (ssRNA) resulting from in vitro transcription. ssRNA was used as the template for the performance of RT-PCR amplification, yielding a correct 220 bp product. (E) Expected result from the sequencing amplicon using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus in 14 sinpro clones. (F) Expected result from the sequencing amplicon in a pool of infected cells using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus.
Mfei Xmai, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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r3589v  (New England Biolabs)
94
New England Biolabs r3589v
Rational design and the experimental validation of the LIS-seq workflow (A) Schematic representation of the experimental strategy of the establishment of single provirus-integrated cellular clones (sinpro clones). A total of 14 clones, in which proviruses demonstrated different transcriptional phenotypes were assigned to four different groups, including the active group (the A group, 4 clones), the attenuated active group (the A-group, 6 clones), the silent group (the S group, 3 clones) and the fluctuation group (the F group, 1 clone) and applied to LIS-seq for the identification of HIV integration sites. (B) Schematic representation of the experimental workflow of LIS-seq. Genomic DNA isolated from sinpro clones was digested with restriction enzymes, HpyCH4III and BplI, followed by in vitro transcription, and RT-PCR amplification with primers embedded with Illumina adaptor sequences. Amplicons are sequenced as 50 bp single reads on a NovaSeq 6000 sequencer (Illumina). (C) Verification of restriction enzyme digestion of genomic DNA isolated from sinpro clones. Genomic DNA is either subjected to BplI plus HpyCH4III (lane 1) or BplI plus HpyCH4III as well <t>as</t> <t>MfeI-HF</t> plus Hpy166I (lane 2). Of note, genomic DNA is digested independently by both pairs of restriction enzymes shown in lane 2. (D) Verification of the production of single-stranded RNA (ssRNA) resulting from in vitro transcription. ssRNA was used as the template for the performance of RT-PCR amplification, yielding a correct 220 bp product. (E) Expected result from the sequencing amplicon using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus in 14 sinpro clones. (F) Expected result from the sequencing amplicon in a pool of infected cells using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus.
R3589v, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mfei bamhi  (New England Biolabs)
99
New England Biolabs mfei bamhi
Rational design and the experimental validation of the LIS-seq workflow (A) Schematic representation of the experimental strategy of the establishment of single provirus-integrated cellular clones (sinpro clones). A total of 14 clones, in which proviruses demonstrated different transcriptional phenotypes were assigned to four different groups, including the active group (the A group, 4 clones), the attenuated active group (the A-group, 6 clones), the silent group (the S group, 3 clones) and the fluctuation group (the F group, 1 clone) and applied to LIS-seq for the identification of HIV integration sites. (B) Schematic representation of the experimental workflow of LIS-seq. Genomic DNA isolated from sinpro clones was digested with restriction enzymes, HpyCH4III and BplI, followed by in vitro transcription, and RT-PCR amplification with primers embedded with Illumina adaptor sequences. Amplicons are sequenced as 50 bp single reads on a NovaSeq 6000 sequencer (Illumina). (C) Verification of restriction enzyme digestion of genomic DNA isolated from sinpro clones. Genomic DNA is either subjected to BplI plus HpyCH4III (lane 1) or BplI plus HpyCH4III as well <t>as</t> <t>MfeI-HF</t> plus Hpy166I (lane 2). Of note, genomic DNA is digested independently by both pairs of restriction enzymes shown in lane 2. (D) Verification of the production of single-stranded RNA (ssRNA) resulting from in vitro transcription. ssRNA was used as the template for the performance of RT-PCR amplification, yielding a correct 220 bp product. (E) Expected result from the sequencing amplicon using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus in 14 sinpro clones. (F) Expected result from the sequencing amplicon in a pool of infected cells using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus.
Mfei Bamhi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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restriction endonuclease mfei hf  (New England Biolabs)
94
New England Biolabs restriction endonuclease mfei hf
Rational design and the experimental validation of the LIS-seq workflow (A) Schematic representation of the experimental strategy of the establishment of single provirus-integrated cellular clones (sinpro clones). A total of 14 clones, in which proviruses demonstrated different transcriptional phenotypes were assigned to four different groups, including the active group (the A group, 4 clones), the attenuated active group (the A-group, 6 clones), the silent group (the S group, 3 clones) and the fluctuation group (the F group, 1 clone) and applied to LIS-seq for the identification of HIV integration sites. (B) Schematic representation of the experimental workflow of LIS-seq. Genomic DNA isolated from sinpro clones was digested with restriction enzymes, HpyCH4III and BplI, followed by in vitro transcription, and RT-PCR amplification with primers embedded with Illumina adaptor sequences. Amplicons are sequenced as 50 bp single reads on a NovaSeq 6000 sequencer (Illumina). (C) Verification of restriction enzyme digestion of genomic DNA isolated from sinpro clones. Genomic DNA is either subjected to BplI plus HpyCH4III (lane 1) or BplI plus HpyCH4III as well <t>as</t> <t>MfeI-HF</t> plus Hpy166I (lane 2). Of note, genomic DNA is digested independently by both pairs of restriction enzymes shown in lane 2. (D) Verification of the production of single-stranded RNA (ssRNA) resulting from in vitro transcription. ssRNA was used as the template for the performance of RT-PCR amplification, yielding a correct 220 bp product. (E) Expected result from the sequencing amplicon using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus in 14 sinpro clones. (F) Expected result from the sequencing amplicon in a pool of infected cells using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus.
Restriction Endonuclease Mfei Hf, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Rational design and the experimental validation of the LIS-seq workflow (A) Schematic representation of the experimental strategy of the establishment of single provirus-integrated cellular clones (sinpro clones). A total of 14 clones, in which proviruses demonstrated different transcriptional phenotypes were assigned to four different groups, including the active group (the A group, 4 clones), the attenuated active group (the A-group, 6 clones), the silent group (the S group, 3 clones) and the fluctuation group (the F group, 1 clone) and applied to LIS-seq for the identification of HIV integration sites. (B) Schematic representation of the experimental workflow of LIS-seq. Genomic DNA isolated from sinpro clones was digested with restriction enzymes, HpyCH4III and BplI, followed by in vitro transcription, and RT-PCR amplification with primers embedded with Illumina adaptor sequences. Amplicons are sequenced as 50 bp single reads on a NovaSeq 6000 sequencer (Illumina). (C) Verification of restriction enzyme digestion of genomic DNA isolated from sinpro clones. Genomic DNA is either subjected to BplI plus HpyCH4III (lane 1) or BplI plus HpyCH4III as well as MfeI-HF plus Hpy166I (lane 2). Of note, genomic DNA is digested independently by both pairs of restriction enzymes shown in lane 2. (D) Verification of the production of single-stranded RNA (ssRNA) resulting from in vitro transcription. ssRNA was used as the template for the performance of RT-PCR amplification, yielding a correct 220 bp product. (E) Expected result from the sequencing amplicon using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus in 14 sinpro clones. (F) Expected result from the sequencing amplicon in a pool of infected cells using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus.

Journal: STAR Protocols

Article Title: An in vitro transcription-based protocol for mapping HIV integration sites using lentiviral integration site sequencing

doi: 10.1016/j.xpro.2025.104284

Figure Lengend Snippet: Rational design and the experimental validation of the LIS-seq workflow (A) Schematic representation of the experimental strategy of the establishment of single provirus-integrated cellular clones (sinpro clones). A total of 14 clones, in which proviruses demonstrated different transcriptional phenotypes were assigned to four different groups, including the active group (the A group, 4 clones), the attenuated active group (the A-group, 6 clones), the silent group (the S group, 3 clones) and the fluctuation group (the F group, 1 clone) and applied to LIS-seq for the identification of HIV integration sites. (B) Schematic representation of the experimental workflow of LIS-seq. Genomic DNA isolated from sinpro clones was digested with restriction enzymes, HpyCH4III and BplI, followed by in vitro transcription, and RT-PCR amplification with primers embedded with Illumina adaptor sequences. Amplicons are sequenced as 50 bp single reads on a NovaSeq 6000 sequencer (Illumina). (C) Verification of restriction enzyme digestion of genomic DNA isolated from sinpro clones. Genomic DNA is either subjected to BplI plus HpyCH4III (lane 1) or BplI plus HpyCH4III as well as MfeI-HF plus Hpy166I (lane 2). Of note, genomic DNA is digested independently by both pairs of restriction enzymes shown in lane 2. (D) Verification of the production of single-stranded RNA (ssRNA) resulting from in vitro transcription. ssRNA was used as the template for the performance of RT-PCR amplification, yielding a correct 220 bp product. (E) Expected result from the sequencing amplicon using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus in 14 sinpro clones. (F) Expected result from the sequencing amplicon in a pool of infected cells using LIS-seq. 2.0% (wt/vol) agarose gel displaying a faint PCR smear corresponding to fragments of different lengths harboring the integration site of the provirus.

Article Snippet: MfeI-HF , New England Biolabs , R3589S.

Techniques: Biomarker Discovery, Clone Assay, Isolation, In Vitro, Reverse Transcription Polymerase Chain Reaction, Amplification, Sequencing, Agarose Gel Electrophoresis, Infection