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Here we describe a number of mechanistic insights gained from an improved dRNA-seq approach that distinguished sites of transcription initiation without erasing the secondary transcriptome using TEX, an enzyme that in our hands can degrade a substantial proportion of 5′-triphosphorylated RNA under the conditions recommended by the vendor (Additional file 11).
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By using density-dependent transition frequency shifts, we were able to spectroscopically distinguish sites with different occupation numbers and to directly image sites with occupation numbers from one to five, revealing the shell structure of the Mott insulator phase.
We filtered all nesting sites to distinguish sites with confirmed, quantified nesting activity (i.e. counts) from those without quantified counts since 2000.
The first PCA axis accounts for 38.1% of total variance explained, and conveniently distinguishes sites with high Nr deposition (positive scores) from those more influenced by climate warming (negative scores).
Richness metrics varied in their ability to distinguish sites.
TALENs are highly specific and can distinguish sites, which differ only in two mismatched bases [ 13, 54].
The core new result here is the crystal structure of the complex of Norrin with Fz4CRD/SOS and studies attempting to distinguish sites of GAG and LRP5/6 binding.
The significance of a property for distinguishing sites from negative sites is calculated over all properties in all shells, and naïve Bayes [ 28] is used to weight the properties most informative for distinguishing the positive and negative sites.
To some extent, the ability to distinguish sites was strongest with % non-insect taxa, with site 1P (in both spring and summer) having a higher metric value than other sites.
MS/MS methods can be used to identify and distinguish site-specific modifications.
To distinguish site-specific binding at these putative polyadenylation sites, from broadly distributed, potentially nonspecific, interactions across transcript bodies, we generated a "peak sharpness" score.
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