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The published Brachypodium whole genome shotgun genome sequence [7] was derived by assembly of end- sequence derived from sized multiple insert clones, including many clones from the BAC libraries described in this study.
With the expressed sequence tag (EST) approach [ 14, 15] expression patterns are analyzed by sequencing many clones from cDNA libraries.
All clones were sequenced from the 3' end ; in addition, 5' sequencing was carried on many clones from the libraries of highest quality or most relevant to our research goals.
Unfortunately, we were not able to obtain sequences from either 5' or 3' ends of many clones from this library, probably due to polyA or polyT sequences in non-coding regions, suggesting that these clones may contain full coding sequences.
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Clonogenicity assay showed that after Dox induction, twice as many clones formed from dissociated iNANOG single cells (Fig. 5H and 5I).
Similar observations, with an expectedly higher hit frequency in sequence-based screening compared to function-based screening, were made for the five enzyme classes (Table 1), suggesting that many clones identified from sequence-based screening were not expressed or expressed in an inactive form in the E. coli heterologous host.
In previous studies, we accumulated a number of 5'-end sequences of many clones derived from the oligo-capped cDNA libraries of the brain with high mRNA complexity, and determined approximately 1,500 full insert sequences of the clones whose 5'-end sequences showed no significant similarity to sequences in the public databases [ 5, 6].
Most of these cases are the result of nonoverlap between the clusters, which is not surprising, given the fragmentary nature of EST evidence and that many clones were sequenced from both the 5' and 3' directions.
We therefore chose many clones at random from the population samples that had been stored at generations 500, 1000, and 1500 generations, and we sequenced the BoxG1 region in each.
For each MHC locus, regardless of how many clones were sequenced from an individual, no more than 2 alleles were observed in an individual, a strong indicator that we amplified single loci in all cases.
This little overlap confirms the utility of combining cDNA and SSH libraries to identify new genes expressed in Eucalyptus secondary xylem: the SSH libraries contain many clones not recovered from the total cDNA library. Figure 2B illustrates the low number of overlapping sequences between the four different SSH libraries.
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