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| Status |
Public on Aug 01, 2018 |
| Title |
Whole genome mapping of DNA G-quadruplexes in multiple species by G4-seq |
| Organisms |
Escherichia coli; Cereibacter 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.
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| 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).
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| Contributor(s) |
Marsico G, Chambers VS, Sahakyan A, Boutell JM, Di Antonio M, Balasubramanian S |
| Citation(s) |
30892612, 37094040 |
| Submission date |
Feb 13, 2018 |
| Last update date |
Aug 11, 2023 |
| 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 |
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| Platforms (12)
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| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
| GPL18133 |
Illumina HiSeq 2500 (Escherichia coli) |
| GPL18245 |
Illumina HiSeq 2500 (Caenorhabditis elegans) |
| GPL18413 |
Illumina HiSeq 2500 (Danio rerio) |
| GPL18841 |
Illumina HiSeq 2500 (Rhodobacter sphaeroides) |
| GPL21078 |
Illumina HiSeq 2500 (Plasmodium falciparum) |
| GPL24609 |
Illumina HiSeq 2500 (Leishmania major) |
| GPL24610 |
Illumina HiSeq 2500 (Trypanosoma brucei) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA434023 |
| SRA |
SRP132824 |
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