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An RT PCR product reproducibly amplified from cDNA of the tumour containing 104C>G showed increased electrophoretic mobility relative to a control fragment amplified from TERT-NHUC cDNA (Fig. 4A).
These USSs were designed to contain the most common base at each position of the extended USSs described above; a control fragment contained a randomized version of the H. influenzae USS sequence.
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A negative control fragment was also analyzed in the same way.
The exon 19 Bi-PASA assay included a PCR control fragment that was always amplified indicating the integrity of the isolated DNA from microdissected clinical tissue samples.
The methylated DNA fragment and an unmethylated control fragment were each ligated into the pGL3-Basic vector prepared by BglII/ HindIII digestion.
The NA1 assay included the two ARMS primers IIIB-NA1F and IIIB-NA1R, and an internal control (fragment of FCGR3A and FCGR3B) was amplified by IIIB-NA1PF and IIIB-NA1PR.
Frozen tumor tissue (TT) and paired normal tissue (NT) were collected from 21 CRC patients; normal tissue was obtained remote from the tumor, near the section boundary; for tumor tissue, an adjacent control fragment was embedded in paraffin, cut and stained with hemalun-eosin-safran to estimate the percentage of cancerous cells (on average 55%).
Importantly, both antibodies turned out to be highly specific with a recovery rate of a total methylated control fragment from input DNA exceeding 45% using the anti-5meC mAb, whereas it was below 2.5% for total hydroxymethylated control DNA and below 1% for unmodified control DNA.
Figure 5 Immunohistochemistry. Demonstrating NIS in the liver tumor tissue of representative mice implanted with a line B tumor fragment (A and C) and a line N negative control fragment (B and D).
DNA of all strains yielded successful amplification of a 1 kb control fragment.
To assess the ligation efficiency, a short DNA control fragment was used for initial ligation reactions (Supporting Information, Table S1).
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