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Unconformity K-1A bound Sequence 2A (lacustrine and fluvial systems) and Sequence 2B (alluvial deposits) in Bauru Basin whereas in the Sanfranciscana and Parecis basins this unconformity marks the transition from alluvial system to aeolian system (Sequences 2A and 2B).
Still, the large majority of TF binding differences are not associated with genetic changes during evolution to the directly bound sequence motifs, and shared TF binding peaks with conserved intensity (discussed below) were more likely to show depletion of nucleotide substitutions and heightened sequence constraint.
This inequality formally arises from (1.1) and later we show that it can provide an upper bound sequence for any solution of (1.1).
The affinity of each transcription factor for DNA varies considerably with the precise bound sequence, even among known in vivo targets [7], [8].
Both ChIP datasets demonstrate that HLH-1 can be detected just upstream of the TSS of thousands of potential target genes, that an E-box (CANNTG) is the dominant over-represented motif in these bound sequence intervals, and the genes associated with binding sites are enriched in those known to be expressed in bodywall muscle.
Although individual mutations in bound sequence motifs can influence TF binding, most binding differences occur in the absence of nearby sequence variations.
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The Table summarizes the total number of hits found by all the PWMs in both GATA-3 bound sequences and in not bound sequences.
As a pair, the central repeat regions of TALENs determine the DNA binding specificity for the two sub-target sites; and the dimeric non-specific FokI cleavage domains cause a DNA double strand break (DSB) between the bound sequences.
Our construction of testing data is similar: we choose the next 500 bound sequences and 500 random unbound sequences.
Again, the new Nanog motif provided a significantly better fit to the ChIP-seq counts of the Nanog bound sequences than the other motifs (Figure 2B, Nanog-500).
After five washings of 500 µl DMEM, bound sequences were recovered in 300 µl of SDS 1%, and the amount of radioactivity recovered was counted.
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