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Series GSE99205 Query DataSets for GSE99205
Status Public on Nov 15, 2017
Title Chromatin immunoprecipitation for genome-wide mapping of endogenous G-quadruplex DNA structures
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary G-rich DNA sequences can form four-stranded G-quadruplex (G4) secondary structures and are linked to fundamental biological processes such as transcription, replication and telomere maintenance. G4s are also implicated in promoting genome instability, cancer and other diseases. Here, we describe a detailed G4 ChIP-seq method that robustly enables the determination of G4 structure formation genome-wide in chromatin. This protocol adapts traditional ChIP-seq for the detection of DNA secondary structures through the use of a G4-structure-specific phage display antibody with refinements in chromatin immunoprecipitation followed by high-throughput sequencing. Beginning with chromatin isolation and antibody preparation the entire protocol can be completed in less than 1 week including computational analysis.
Overall design One cell line analysed with G4 ChIP-seq to detect the presence of G-Quadruplexes. Experiment performed in triplicates.
Contributor(s) Hänsel-Hertsch R, Spiegel J, Marsico G, Tannahill D, Balasubramanian S
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Submission date May 23, 2017
Last update date May 15, 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)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (4)
GSM2635752 BG4-ChIP-rep1
GSM2635753 BG4-ChIP-rep2
GSM2635754 BG4-ChIP-rep3
BioProject PRJNA387558
SRA SRP107851

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Supplementary file Size Download File type/resource 50.4 Mb (ftp)(http) BW 19.8 Mb (ftp)(http) BW 42.9 Mb (ftp)(http) BW
GSE99205_README.txt 264 b (ftp)(http) TXT 20.9 Mb (ftp)(http) BW
GSE99205_common_HaCaT_G4_ChIP_peaks_RNase_treated.bed.gz 96.8 Kb (ftp)(http) BED
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Processed data are available on Series record

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