|
| Status |
Public on May 15, 2014 |
| Title |
Afu UDG Predigestion Beseq replicate 1 (Y7092) |
| Sample type |
SRA |
| |
|
| Source name |
S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: MATalpha can1∆::STE2pr-Sp_his5 lyp1∆ ura3∆0 leu2∆0 his3∆1 met15∆0 ung1::natMX dut1-1::URA3
enzyme treatment: UDG-New England Biolabs, Y7092 starter strain from Dr. C. Boone
|
| 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 HiSeq 2000 |
| |
|
| 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 |
| E-mail(s) |
jay.hesselberth@cuanschutz.edu
|
| 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 |
GPL13821 |
| Series (1) |
| GSE51361 |
High resolution mapping of modified nucleobases in DNA using excision repair enzymes |
|
| Relations |
| BioSample |
SAMN02380481 |
| SRA |
SRX366882 |
