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Series GSE63874 Query DataSets for GSE63874
Status Public on Jul 19, 2015
Title High-throughput sequencing of DNA G-quadruplex structures in the human genome
Organism Homo sapiens
Experiment type Other
Summary Nucleic acid secondary structures play a critical role in the regulation of biological processes. Genome-wide detection of DNA and RNA secondary structures is essential to identify pathways that are regulated by nucleic acid folding. There are no methods to interrogate DNA secondary structure formation on a genome-wide scale. We present G4-Seq, a method that applies the concept of polymerase interference at G-quadruplex (G4) DNA secondary structures to a human genome scale by massively parallel array-sequencing. Our approach generated a high-resolution map of more than 700,000 distinct G4s in the human genome, including non-canonical structural variants with bulges or extended loops, which are difficult to predict by classical approaches. This experimental map reveals many previously uncharacterized G4 structures in functional genomic regions, of which we highlight those associated with cancer, that include oncogenes, tumor suppressors and somatic copy-number alterations.
Overall design 4 library samples, 150 base pairs custom protocol (G4-Seq) sequenced as two-times single-end reads on HiSeq 2500: 2 replicates for Na+ (Read-1) and K+ (Read-2); 2 replicates for Na+ (Read-1) and PDS+Na+ (Read-2).
Contributor(s) Chambers VS, Marsico G, Boutell JM, Di Antonio M, Smith GP, Balasubramanian S
Citation(s) 26192317, 29109402
Submission date Dec 04, 2014
Last update date Jul 19, 2019
Contact name Giovanni Marsico
Organization name CRUK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (4)
GSM1558753 Na_K_1
GSM1558754 Na_K_2
GSM1558755 Na_PDS_1
BioProject PRJNA269309
SRA SRP050569

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE63874_Na_K2_all_minus_cov.tdf 573.3 Mb (ftp)(http) TDF
GSE63874_Na_K2_all_plus_cov.tdf 579.7 Mb (ftp)(http) TDF
GSE63874_Na_K_12_minus.bedGraph.gz 1.0 Gb (ftp)(http) BEDGRAPH
GSE63874_Na_K_12_minus.tdf 501.1 Mb (ftp)(http) TDF
GSE63874_Na_K_12_plus.bedGraph.gz 1.1 Gb (ftp)(http) BEDGRAPH
GSE63874_Na_K_12_plus.tdf 505.9 Mb (ftp)(http) TDF
GSE63874_Na_K_PDS_minus_hits_intersect.bed.gz 1.5 Mb (ftp)(http) BED
GSE63874_Na_K_PDS_plus_hits_intersect.bed.gz 1.5 Mb (ftp)(http) BED
GSE63874_Na_K_all_minus_cov.tdf 574.9 Mb (ftp)(http) TDF
GSE63874_Na_K_all_plus_cov.tdf 581.3 Mb (ftp)(http) TDF
GSE63874_Na_K_minus_hits_intersect.bed.gz 1.9 Mb (ftp)(http) BED
GSE63874_Na_K_plus_hits_intersect.bed.gz 1.9 Mb (ftp)(http) BED
GSE63874_Na_PDS2_all_minus_cov.tdf 586.8 Mb (ftp)(http) TDF
GSE63874_Na_PDS2_all_plus_cov.tdf 593.1 Mb (ftp)(http) TDF
GSE63874_Na_PDS_12_minus.bedGraph.gz 1.0 Gb (ftp)(http) BEDGRAPH
GSE63874_Na_PDS_12_minus.tdf 483.2 Mb (ftp)(http) TDF
GSE63874_Na_PDS_12_plus.bedGraph.gz 1.0 Gb (ftp)(http) BEDGRAPH
GSE63874_Na_PDS_12_plus.tdf 487.7 Mb (ftp)(http) TDF
GSE63874_Na_PDS_all_minus_cov.tdf 584.1 Mb (ftp)(http) TDF
GSE63874_Na_PDS_all_plus_cov.tdf 590.5 Mb (ftp)(http) TDF
GSE63874_Na_PDS_minus_hits_intersect.bed.gz 2.6 Mb (ftp)(http) BED
GSE63874_Na_PDS_plus_hits_intersect.bed.gz 2.6 Mb (ftp)(http) BED
GSE63874_README.txt 5.9 Kb (ftp)(http) TXT
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