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Four biological replicates were collected and 5 μg of total RNA was used from each sample for library preparation.
The fragmented input genomic DNA (I) and enriched E5 fraction (E) were isolated from each sample for library preparation and sequencing using SOLiD™ v3 and v4 chemistry according to the manufacturer's protocols (Life Technologies).
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The NEXTflex Dual-Indexed DNA Barcodes are designed for multiplexing of up to 192 samples for library preparation.
DJI generated samples for library construction.
FL generated samples for library construction.
Aerial parts of cold-acclimated plants were sampled for Library 2 and roots of both cold-acclimated and salt-stressed plants were sampled for Library 3.
Mono-nucleosomal DNA fragments of approximately 100 200 bp were gel-purified from both samples for library construction.
In this study, we benchmark our protocol on DNA samples used in the International HapMap Project with known HLA types: 270 samples for library construction-based barcoding and 95 samples for the barcoded PCR method.
Further, the list of genes with the high number of matching unigenes (Table 2) was notably full of genes expected to be highly expressed in the tissues sampled for library construction.
Samples for library generation were taken from multiple tissues from adult fish from either 1) the same collection as fish enrolled in the breeding programs, 2) from parents of family fish, 3) from F1 juveniles produced by the breeding programs.
The first number indicates the genotype (e.g. 816) and the number after the point indicates the sample used for library preparation (where multiple samples were collected, e.g. 816.1, 816.3) The other gene corresponds to the Arabidopsis gene HARDY (HRD).
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