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Each biological replicate was pooled from 9 plants, and there were 3 biological replicates per treatment.
After extraction, total RNA from each biological replicate was pooled equally in order to obtain 8 μg of total RNA in 50 μL for each treatment and used for mRNAseq library preparation using mRNA-Seq-8 Saccordingp Kito(Illumina, USA) according thethe manufacturer's instructions.
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Each Hi-C library was sequenced using paired-end sequencing on an Illumina HiSeq 3000 in two technical replicates; reads for each biological replicate were pooled and mapped to the human genome (version hg19) using hiclib63 (https://bitbucket.org/mirnylab/hiclib/).org/mirnylab/hiclib/
Four μg of each biological replicate were pooled together and freeze-dried.
Six libraries from a biological replicate were pooled on the same HiSeq2000 lane.
Three independent preparations of mRNA for each biological replicate were pooled to eliminate inconsistencies due to sampling.
Three independent preparations of mRNA for each biological replicate were pooled to eliminate the inconsistent variation with sampling.
Separated skins and pulp of all the berries of each biological replicate were pooled (without seeds) and ground in a frozen mortar and pestle.
After extraction, total RNAs from each biological replicate were pooled in equal quantity to obtain a total RNA mixture representative of 180 individuals.
Equal amounts of total RNA from each biological replicate were pooled and used for isolation of the small RNA fraction using the miRVana™ miRNA Isolation kit (Ambion®).
At each time point, three biological replicates were designed; the samples of each biological replicate were pooled from 10 plants, the plants being randomly selected to avoid any potential effects of position within the growth room.
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