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DDX3X RNA binding was identified by structural alignment between DDX3X and DDX4 using Chimera.
AnnexinV binding was identified by flow cytometry using an AnnexinV-FITC staining procedure following the manufacturer's instructions (Becton Dickinson).
Annexin-V binding was identified by flow cytometry using Annexin-V-FITC staining, following the manufacturer's instructions as previously described (Becton Dickinson, San Jose, CA, USA).
H4K5Ac binding was identified by ChIP-Seq and was calculated by comparing the control and METH-treated groups after corrections for DNA inputs.
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Median normalization of the log2 values of the ratio of signal to mock (precipitated DNA without antibody) was performed across the three-ChIP-chip arrays followed by a mean centralization to 0. Regions of Pol II binding were identified by the ChIPOTle sliding window method [22]; a window size of 1 Kb was used with a step size of 50 bp.
The amino acids contributing to the antibody binding were identified by mutational analysis [ 22, 23].
Gene Ontology categories enriched for Dali binding were identified by intersecting regulatory regions for known coding genes with Dali binding sites.
Gene ontology categories enriched for Paupar binding were identified by intersecting regulatory regions for known coding genes with Paupar binding sites.
The unique cDNA sequence for the variable domains (VH and VL) containing the complementarity-determining regions (hypervariable domains) responsible for antigen binding were identified by comparison of multiple sequenced clones to the mouse IG set from the ImMunoGeneTics information system for V-QUEry and STandardization (IMGT/V-QUEST) reference directory (28) (Fig. 3 C ).
P450 oxygen binding motif was identified by searching for the sequence motif '[A/G]G* [E/D]T [T/S]'(represents either or).
No modification of the luciferase activity was observed for a sequence derived from the negative control CASP3 regulatory region (where no conserved binding site was identified by the oPOSSUM program).
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