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Eight 8p11-12 genes (ASH2L, BAG4, BRF2, DDHD2, LSM1, PROSC, RAB11FIP1, and WHSC1L1) together with the a priori selected FGFR1 gene, highly discriminated FGFR1 amplification (area under the receiver operating characteristic curve ≥0.82, all genes and all cohorts).
The contaminated areas included the amplification area, air conditioning, keyboard and screen of the ProbeTec instrument, door handles, work bench, and fridge.
RNA was DNAse treated and digested before cDNA synthesis with Eco 130I, which cuts the DNA in the middle of the amplification area in order to get rid of possible genomic contamination.
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As rtPCR was performed as a sealed system, amplification was also performed in the main laboratory with the tubes only opened in the contained post-amplification area [ 10].
For PCR amplification, 15 μl of reconstituted ready-to-use PCR mix (provided with the kit) was added to PCR tubes in a DNA-free and PCR amplicon-free pre-amplification area.
The PCR product was denaturated for 1 min at 95°C and immediately cooled on ice for no more than 1 min. Then, 5 μl of PCR product was added to 40 μl of pre-heated (55°C) running solution in a 1.5 ml tube (post-amplification area).
If anything needed to be re-used and go against the unidirectional flow, such as PCR racks or bottles, they were decontaminated overnight in a 1 100 dilution of Trigene® Advance (MediChem International Ltd ,UK) before returning to the pre-amplification area [ 10].
Carryover contamination was prevented by the strict implementation of the unidirectional flow from pre-amplification to post-amplification areas, with only sealed tubes and racks travelling down the workflow [ 10].
However, its relative complexity, the requirement of pre-amplification areas and the need of staff experienced with molecular biology methods makes it suitable mainly for modern molecular microbiology laboratories with high capacity diagnostics.
Silver in situ hybridisation confirmed HER2 amplification in area 1 and lack of amplification in area 2, with sharp borders between the two areas.
One sample presented a heterogeneous labeling along the tumor field with some areas presenting gene amplification and areas with normal signal (non-amplified).
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