NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE51361 Query DataSets for GSE51361
Status Public on May 15, 2014
Title High resolution mapping of modified nucleobases in DNA using excision repair enzymes
Organisms Escherichia coli; Saccharomyces cerevisiae
Experiment type Other
Summary Data from Excision-seq experiments to map deoxyuridine and pyrimidine dimers in S. cerevisiae and E. coli
 
Overall design For uracil mapping in pre-digestion Excision-seq, uracil was excised from genomic DNA from dut ung yeast and bacteria yielding double-stranded DNA fragments. Adapters were ligated to these fragments for Illumina library preparation. Using this method, the number of reads at a genomic location corresponds to the quantity of dU at that location. In post-digestion Excision-seq, uracil-containing library fragments are destroyed by UDG treatment, thus coverage is inversely proportional to uracil content. For pyrimidine dimer Excision-seq, yeast were irradiated with high doses of UVC light to generate a large number of DNA modifications.  Using the excision repair enzyme UVDE from S. pombe, we excised pyrimidine dimers, cutting the phosphodieseter bond to release small double stranded fragments. These fragments were repaired with either CPD photolyase or 6-4 photolyase to generate independent libraries for each modification type. Illumina adapters were ligated to these fragments for library preparation. Using this method the number of reads at a genomic location corresponds to the quantity of the 3' pyrimidine of the dimer.
 
Contributor(s) Hesselberth J
Citation(s) 25015380
Submission date Oct 17, 2013
Last update date Mar 13, 2019
Contact name Jay R. Hesselberth
E-mail jay.hesselberth@gmail.com
Phone 303-724-5384
Organization name University of Colorado School of Medicine
Department Biochemistry and Molecular Gentetics
Lab Jay Hesselberth
Street address 12801 E 17TH AVE
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
 
Platforms (4)
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
GPL10328 Illumina Genome Analyzer II (Escherichia coli)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (11)
GSM1243338 CPD Beseq replicate 1
GSM1243339 6-4pp Beseq replicate 1
GSM1243340 CPD Beseq replicate 2
Relations
BioProject PRJNA223409
SRA SRP031833

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
GSE51361_RAW.tar 191.3 Mb (http)(custom) TAR (of BEDGRAPH)
Raw data are available in SRA
Processed data provided as supplementary file

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