Journal: The Malaysian Journal of Medical Sciences : MJMS

Article Title: Construction and Cloning of Reporter-Tagged Replicon cDNA for an In Vitro Replication Study of Murine Norovirus-1 (MNV-1)

doi: 10.21315/mjms2017.24.6.4

Figure Lengend Snippet: Gel electrophoresis showing a second overlapping-extension PCR (OE-PCR) product prior to gel purification. The bands on the farthest left side belong to a 1-kb DNA ladder (Promega, USA). The third and fifth lanes show the second OE-PCR product with the amplicon size being 3017 bps (top band–red circle)

Article Snippet: The bands on the farthest left side belong to a 1-kb DNA ladder (Promega, USA).

Techniques: Nucleic Acid Electrophoresis, Overlap Extension Polymerase Chain Reaction, Gel Purification, Amplification

Journal: The Malaysian Journal of Medical Sciences : MJMS

Article Title: Construction and Cloning of Reporter-Tagged Replicon cDNA for an In Vitro Replication Study of Murine Norovirus-1 (MNV-1)

doi: 10.21315/mjms2017.24.6.4

Figure Lengend Snippet: (A) Gel electrophoresis following restriction enzyme analysis of three backbones of MNV-1 cDNA clone vectors. The bands on the farthest left side belong to a 1-kb DNA ladder (NEB, USA). The second lane shows the undigested MNV-1 cDNA clone (11810 bps). The third lane shows the digested MNV-1 wt, whereas the fourth lane shows the digested MNV-1 F/S. The fifth lane shows the digested MNV-1 ΔNS7. (B) Gel electrophoresis following the digestion of the insert (2nd OE-PCR product). The first lane from the left shows a 1-kb DNA ladder (NEB, USA). The second lane shows the undigested insert, whereas the third lane shows the digested insert (red circle)

Article Snippet: The bands on the farthest left side belong to a 1-kb DNA ladder (Promega, USA).

Techniques: Nucleic Acid Electrophoresis, Overlap Extension Polymerase Chain Reaction

Journal: The Malaysian Journal of Medical Sciences : MJMS

Article Title: Construction and Cloning of Reporter-Tagged Replicon cDNA for an In Vitro Replication Study of Murine Norovirus-1 (MNV-1)

doi: 10.21315/mjms2017.24.6.4

Figure Lengend Snippet: Gel electrophoresis following restriction enzyme analysis of cloned cDNA from positive clones. Three backbones of MNV-1 cDNAs; wt, F/S and ΔNS7 were obtained after large-scale production and purification (midiprep). The bands on the farthest left side belong to a 1-kb DNA ladder (NEB, USA). The second and third lanes represent the undigested MNV-1 cDNA clone (11810bps) and the second OE-PCR insert product (3017bps), respectively. The fourth, fifth and sixth lanes show the digested cloned cDNA of pT7. MNV-secNluc2A-VP2-3′Rz (wt); pT7. MNV-secNluc2A-VP2-3′Rz (F/S); and pT7. MNV-secNluc2A-VP2-3′Rz (ΔNS7), respectively. Successful restriction enzyme digestion released vectors (10168bps) and inserts (2292bps) of the correct size.

Article Snippet: The bands on the farthest left side belong to a 1-kb DNA ladder (Promega, USA).

Techniques: Nucleic Acid Electrophoresis, Clone Assay, Purification, Overlap Extension Polymerase Chain Reaction

Journal: Mobile DNA

Article Title: Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome

doi: 10.1186/s13100-019-0148-5

Figure Lengend Snippet: Approaches to PCR validation of insertions. a Agarose gel electrophoresis of a somatic PCR validation. Three lanes are shown: [L] 2-log ladder (NEB), [N] normal DNA, [T] tumor DNA. An upper band marked by a black arrow is present in the tumor but absent in the normal sample which confirms a somatic L1 insertion occurred in the tumor. b Agarose gel of two L1 3’ PCR validations. Five lanes are shown: [L] 2-log ladder (NEB), [F1] forward primer with L1 primer for insertion on 2p16.3, [R1] reverse primer with L1 primer for insertion on 2p16.3, [F2] forward primer with L1 primer for insertion on 9q21.31, [R2] reverse primer with L1 primer for insertion on 9q21.31. For both insertions, only the reverse primer produces a band when paired with the L1 primer, which suggests that both are plus strand insertions. All specific primers were designed approximately 200 bp away from the insertion site. Because the L1 primer is located 150 bp away from the 3′ end of the element, the expected product size for both reactions is approximately 350 bp marked with a gray arrow. The PCR reaction for the 9q21.31 insertion produces a band larger than expected marked with a black arrow. This suggests that a 3′ transduction may have taken place and is confirmed by sending the PCR product for Sanger sequencing. c The illustration shows the relative positions of primers and products for the two L1 insertions from part b. The 9q21.31 insertion in the lower diagram has a 3′ transduction shown as a gold line

Article Snippet: 2-log ladder (NEB, cat. no. N3200S) Qubit dsDNA HS assay kit (ThermoFisher Scientific, cat. no. Q32851) Agilent DNA 1000 kit (Agilent, cat. no. 5067–1504) Agencourt AMPure XP Magnetic Beads (Beckman Coulter, cat. no. A63882) KAPA HTP Library Preparation Kit for Illumina (KAPA Biosystems, cat. no. KK8234).

Techniques: Agarose Gel Electrophoresis, Transduction, Sequencing