Bioinformatic Data on G-Quadruplexes in Genomes

DNA G-quadruplexes

1.  DNA G-quadruplexes in human raw data, supplementary bed files with genomic coordinates and genomic tracks are deposited

(GEO: GSE63874 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63874)

NOTE: genomic coordinates of the DNA-G4 are reported by strand and for each of the following experimental conditions:

• [Na+]_[ K+]: GSE63874_Na_K*.bed
• [Na+]_[PDS]:GSE63874_Na_PDS*.bed
• [K+]_[ Na+]_[PDS]): GSE63874_Na_K_PDS*.bed

For example, the 716,310 OQs are those identified in PDS on both forward and reverse strand. To obtain the list of these distinct quadruplexes, download and decompress the bed files containing PDS in the file name:

GSE63874_Na_K_PDS_minus_hits_intersect.bed
GSE63874_Na_PDS_minus_hits_intersect.bed

GSE63874_Na_K_PDS_plus_hits_intersect.bed
GSE63874_Na_PDS_plus_hits_intersect.bed

Merging and counting by strand provides the individual OQs by strand:

cat *PDS*minus*bed | sortBed -i – | mergeBed -i – |wc -l
356379
cat *PDS*plus*bed | sortBed -i – | mergeBed -i – |wc -l
359932

Note that there is one element more than the number reported in the paper (356379 + 359932 = 716311).