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The selection of microarray probes was performed in two steps using custom software developed in our lab.
Modification of the gene list of microarray probes was described previously [ 66].
Because the RNA fragments contained in our samples were amplified using poly(A) tail primers, the binding probability to the corresponding microarray probes was maximized.
However, we found that the gene model used for design of hac1 microarray probes was incorrect and moreover hac1 has splice variation [ 41] that is not measured by our microarray.
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The target gene regions of microarray probes were retrieved from the annotation file for human U133 Plus 2.0 (http://www.affymetrix.com).
Microarray probes were designed primarily from P. taeda hybridised with cRNA constructed from the close relative P. radiata.
First, microarray probes were optimized by screening 244,000 probes for hybridization with RNA from infected and uninfected macrophages.
A total of 74,179 microarray probes were calibrated using the Gene Meter approach and the transcriptional profiles of 1063 genes that significantly increased in abundance were assembled into a time series spanning from life to 48 or 96 h postmortem.
In addition, single nucleotide polymorphisms (SNPs) were identified and mapped to trees, and SNP microarray probes were designed to enable highly multiplexed genotyping of an unsequenced sample by hybridization.
The "present" and "absent" information of microarray probes were obtained by applying the mas5calls function in biocondutor (http://www.bioconductor.org).
This lack of enrichment indicates that hybridization artifacts due to SNPs within microarray probes are unlikely to affect our results.
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