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To map the cleavage sites in PaSPL and PaAP2 mRNA, total RNAs were extracted from leaves, flower buds and flowers.
To map the cleavage sites in X0 four identical junctions were made, each of which was 5' end-labelled in a different strand.
While the Ephrin receptor 3 details are clearly available in the uniprot to map the cleavage sequence, those of Ephrin receptor 2 is not.
This information was used to design primers to map the cleavage sites precisely using the rapid amplification of cDNA ends (RACE) technique.
Attempts to map the cleavage site(s) more precisely suggested that the cleavage occurs after position 78 in NORE1A in the Proline-rich region, since NORE1A fragment 78 190 is cleaved by H358 cell extract (Figure 2B, lane 6).
However, a fortuitous mutation allowed us to map the cleavage site more accurately.
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Brm-D1 to D4 were the deletions that were used to map the cleavages site of Brm.
Because the eukaryotic mitochondrial ribosomes are thought to have shared a common ancestor with archaebacterial ribosomes, we mapped the cleavage sites onto the predicted secondary structure of the D. discoideum mitochondrial LSU rRNA based on the halobacteria Haloarcula marismortui rRNA structure [33], [50] (Figure 4A).
Brm-D718A/D726A/D728A/D731A/D740,741A were the mutants generated for mapping the cleavage sites.
Using purified N169-T120 Tev-mTALEN, we mapped the cleavage site to the motif at 14 bp from the TAL binding site (motif3, 5′-CTGTG-3′).
Very low abundance signatures including only 1 read was categorized as category 4. For mapping the cleavage site within the miRNA target, a modified procedure for RNA ligase mediated (RACE5' RACE) was performed using the FirstChoice RLM-RACE Kit (Ambion).
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