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Series GSE110582 Query DataSets for GSE110582
Status Public on Aug 01, 2018
Title Whole genome mapping of DNA G-quadruplexes in multiple species by G4-seq
Organisms Escherichia coli; Rhodobacter sphaeroides; Arabidopsis thaliana; Saccharomyces cerevisiae; Leishmania major; Trypanosoma brucei; Plasmodium falciparum; Caenorhabditis elegans; Drosophila melanogaster; Danio rerio; Homo sapiens; Mus musculus
Experiment type Other
Summary The identification of DNA G-quadruplexes (G4s) in the genome is important to study different biological processes in which these structures play a role, such as genome rearrangement, transcriptional regulation and DNA replication. G4-seq allowed the high-throughput experimental mapping of G-quadruplexes in the human genome. We developed here an improved version of this method, named G4-seq2, which we applied to generate G-quadruplexes genomic maps for 12 species, selected as important models organism to study development or as pathogens of clinical relevance. Those multi-species maps, publicly available for the community, will allow to further understand the design principle of G-quadruplex formation in genomic context, to study G-quadruplex biology in those model organisms, to predict ligand targeting for therapeutic usage and to design G-quadruplex computational predictors based on genome-wide experimental measurements.
 
Overall design 24 library samples, 150 base pairs custom protocol (G4-Seq2) sequenced as two-times single-end reads on HiSeq 2500: 12 samples from different species for Li+ (Read-1) and K+ (Read-2); 12 samples from different species for Li+ (Read-1) and PDS+K+ (Read-2).
 
Contributor(s) Marsico G, Chambers VS, Sahakyan A, Boutell JM, Di Antonio M, Balasubramanian S
Citation(s) 30892612
Submission date Feb 13, 2018
Last update date May 09, 2019
Contact name Giovanni Marsico
E-mail(s) persego@gmail.com
Organization name CRUK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platforms (12)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
Samples (24)
GSM3003535 Arabidopsis_Li_K
GSM3003536 Arabidopsis_Li_KPDS
GSM3003537 Celegans_Li_K
Relations
BioProject PRJNA434023
SRA SRP132824

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

Supplementary file Size Download File type/resource
GSE110582_RAW.tar 20.6 Gb (http)(custom) TAR (of BED, BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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