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Northern blotting using a probe for the 3' flanking region of the GSA target showed no signal in either the 35S GS-IR or the CoYMV:GS-IR transgenic line (Figure S4), although both exhibited unequivocal PTGS (Figure S2a, S2b).
We next carried out Southern blotting using a probe that targets the 30 portion of the LUC coding sequence.
A measure of 30 μg of total RNA were analysed by Northern blotting using a probe from the pGem3HR plasmid (Mayer et al, 2005) and Northern with a β-actin probe or ethidium bromide staining was used as loading control.
Two clones were selected following further screening by Southern blotting using a probe located 5' to the targeting vector as described previously [ 26].
DNA was then isolated, digested with SacI, and the fragments analyzed by southern blotting using a probe corresponding to bp +1060 to +1264 relative to the transcription start site.
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Deletion of the genomic sequence was confirmed by Southern blotting using a flanking probe as well as a neomycin probe (Figure 4B).
Potential conditional knockout clones were grown in 10 ml LB/Kan/Sm to saturation followed by genomic DNA extraction, digestion with HindIII/NotI/XbaI and Southern blotting using a MSMEG_6382-specific probe.
DSBs along chromosome VII were detected by Southern blotting using a CRM1 (YGR218W) DNA probe.
G418-resistant clones were isolated and recombination was confirmed by Southern blotting using an internal probe.
For lcp3, cutting with the restriction enzymes NotI and AscI (each has a single restriction site in lcp3), was confirmed by Southern blotting using an lcp3-specific probe.
Following selection with G418, the gene-targeting events (Smg6+/T ESCs) were confirmed by Southern blotting using an external probe upstream of exon 1 after NcoI digestion of the genomic DNA.
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