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A pool to pool probe effect normalization was performed as described by Blenkiron et al. [ 26].
In addition to optimizing the quantity of probe, a range of hybridization and washing temperatures were tested using 2 μg of 78 k shRNA pool probe.
This learning deficit was reflected in the failure of the ATNx1 rats to select preferentially the correct corners on the first swim trial after passive training or to prefer the vicinity of the correct corners over the incorrect corners when allowed to swim around the rectangular pool (Probe Test, Experiment 1).
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Distribution plots generated from the raw, GCbg-corrected, and Loess-normalized signal intensities demonstrated that GCbg-correction served to increase the differentiation between signal from the features corresponding to shRNA pool probes and those features on the GMAP without corresponding partners in the probe pool.
From this finding, we infer that amongst the human shRNA features, the cross-hybridization rate from human 78 k pooled probe would be similar.
Pooled probes were dried to completion using an Eppendorf Vacufuge then fragmented using Fragmentation Reagent (Ambion).
Pooled probes contained 0.1 μg of each BAC DNA, 5 μg salmon sperm DNA, and 6 μg Cot-I DNA.
The HC2 is a pooled-probe, nucleic acid hybridization assay with signal amplification that uses microplate chemiluminescent detection.
Amplicor is a pooled-probe, polymerase-chain reaction (PCR -based test that targets the same HPCR -baseds HC2, and LA is a test-specific primer PCR assay for 37 HPV thats.
This pool, including probe sets that were part of significant prognostic models in all datasets, was selected for the custom array.
Thus, one important challenge in ABPP is expanding the pool of probe molecules to enzyme classes with more complex catalytic activities such as kinases,[ 3, 9] transferases,[ 10] and oxidoreductases[ 11] to extend the proteome coverage.
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