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Sample GSM1243342 Query DataSets for GSM1243342
Status Public on May 15, 2014
Title UDG Predigestion Beseq
Sample type SRA
Source name S. cerevisiae
Organism Saccharomyces cerevisiae
Characteristics strain: MATa leu2-3-112 trp1-289 his7-2 ura3-52 lys1-1 ade2∆ dut1-1 ung1∆::URA3 bar1Δ::kanMX hENt::LEU
enzyme treatment: UDG-New England Biolabs, yeast DNA from Dr. S. Boiteux
Treatment protocol Cells were arrested in S-phase with alpha factor
Growth protocol Yeast cells were grown in YEPD at 30˚ to an OD600 ~1.0
Extracted molecule genomic DNA
Extraction protocol genomic DNA was isolated using SDS and proteinase K followed by RNAseA treatment and DNA precipitation
genomic DNA was treated with Beseq enzymes as stated for samples above. Samples were treated with NEB end repair kit. Samples were A-tailed using Klenow exo- from Enzymatics. Samples were ligated with Illumina Truseq adapters using Enzymatics T4 DNA ligase. Samples were size selected with Invitrogen size select gels. Samples were PCR amplified using barcoded Illumina Truseq primers and Ampure bead purified. Samples were quantitated with Qubit before sequence submission.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer II
Description BE-seq
Data processing Reads were aligned to theUCSC sacCer1 genome using bowtie2
BAM alignment files were processed to genome coverage in bedGraph format using bedtools
bedgraph files were displayed in the UCSC Genome Browser
Genome_build: sacCer1, E. coli K12
Supplementary_files_format_and_content: Genome coverage in bedGraph format
Submission date Oct 17, 2013
Last update date May 15, 2019
Contact name Jay R. Hesselberth
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
Platform ID GPL9377
Series (1)
GSE51361 High resolution mapping of modified nucleobases in DNA using excision repair enzymes
BioSample SAMN02380484
SRA SRX366878

Supplementary file Size Download File type/resource
GSM1243342_UDG_predig.bedGraph.gz 4.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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