GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE103125 Query DataSets for GSE103125
Status Public on Nov 06, 2017
Title High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genome-wide mapping of transcription factor binding is generally performed by chemical protein-DNA crosslinking, followed by chromatin immunoprecipitation and deep sequencing (ChIP-seq). Here we present the ChIP-seq technique based on photochemical crosslinking of protein-DNA interactions by high-intensity ultraviolet (UV) laser irradiation in living mammalian cells (UV-ChIP-seq). UV laser irradiation induces efficient and instant formation of covalent “zero-length” crosslinks exclusively between nucleic acids and proteins that are in immediate contact, thus resulting in a “snapshot” of direct protein-DNA interactions in their natural environment. We applied UV-ChIP-seq for genome-wide profiling of the sequence-specific transcriptional repressor B-cell lymphoma 6 (BCL6) in human diffuse large B-cell lymphoma (DLBCL) cells. Our approach resulted in sensitive and precise protein-DNA binding profiles, highly enriched in canonical BCL6 DNA sequence motifs. UV-ChIP-seq also revealed numerous previously undetectable BCL6 binding sites, particularly in more condensed, inaccessible areas of chromatin.
Overall design Genome-wide mapping of BCL6-DNA interactions by replicate UV-ChIP-seq and corresponding control experiments. To control for enrichment of non-crosslinked protein-DNA interactions we performed ChIP-seq using non-irradiated cells (-UV control ChIP). Furthermore, unspecific antibody binding and input loading was controlled by sequencing of IgG enriched DNA fragments (UV IgG control) and input DNA fragments (UV input DNA) following UV irradiation, respectively. To compare photochemical (UV) with conventional chemical (FA) crosslinking, we performed BCL6 FA ChIP-seq and corresponding control experiments (FA input DNA, FA IgG control).
Contributor(s) Steube A, Saluz HP
Citation(s) 29101361
Submission date Aug 25, 2017
Last update date May 15, 2019
Contact name Arndt Steube
Organization name Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)
Department Cell and Molecular Biology
Lab HPSaluz Lab
Street address Adolf-Reichwein-Strasse 23
City Jena
ZIP/Postal code 07745
Country Germany
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (8)
GSM2754202 BCL6_UV-ChIP-seq_repl1
GSM2754203 BCL6_UV-ChIP-seq_repl2
GSM2754204 UV_input_DNA
BioProject PRJNA400227
SRA SRP116200

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

Supplementary file Size Download File type/resource 551.1 Mb (ftp)(http) BW 330.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap