To prepare inserts (candidate SNP-containing sequences), we performed PCR to amplify DNA fragments covering all SNPs selected from SNPs-seq.
In order to fully characterize the ability of the selected ligands to bind and stabilize the G4 structures originated by the c-MYC and BCL-2 promoter sequences, we performed electrospray ionization mass spectrometry (ESI-MS), Fluorescence Resonance Energy Transfer (FRET) measurements, Circular Dichroism (CD) spectra and polymerase stop assay.
To characterize those sequences, we performed de novo assembly of unmapped reads from WAB56 104.
Using primers designed for the T-DNA LB and RB sequences we performed tail-PCR analysis and determined the insertion location of the gene on chromosome 1 at 5269546 bp or 98 bp of the 3′-UTR of CKX2 (LOC_Os01g10110) (Additional file 3: Figure S3C).
To exclude the human-derived read sequences, we performed an analysis pipeline as follows (Fig. 1A).
Together with previously reported SERA sequences, we performed evolutionary analyses of the gene family.
For comparing data generated by Bayes Serial SimCoal with data extracted directly from mtDNA sequences, we performed statistical test proposed by Voight et al. 2005 [41].
To investigate potential selective pressure for maintaining RNA structural elements within EIAV ERRE sequences, we performed information content analyses using a group of variant EIAV sequences.
To identify TFBS motifs specifically associated with the different sets of sequences, we performed an unsupervised, two-way hierarchical clustering of the relative frequency of each motif (likelihood ratio values) obtained from the Clover analysis.
To ascertain whether databases containing DNA sequences, genome assemblies and trace archive reads were contaminated with human sequences, we performed an in depth search for sequences of human origin in non-human species.
To avoid the potential ambiguity introduced by cross-hybridization of repetitive sequences, we performed the same test using only probes with unique sequences (probes that match only once to the genome as defined by BLAT analysis) [48].
