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Sample GSM5695177 Query DataSets for GSM5695177
Status Public on Jan 01, 2023
Title BY6_HindIII_EcoRI-norm_70_pct_cut_X
Sample type SRA
 
Source name S. cerevisiae/S. pombe cells
Organisms Schizosaccharomyces pombe; Saccharomyces cerevisiae
Characteristics restriction enzyme: EcoRI
digestion degree[%]: 70
Treatment protocol no further treatment of cells prior to harvest; genomic DNA was digested or mock digested with restriction enzymes and sheared by sonication.
Growth protocol Grow 7 * 109 cells of S. cerevisiae or S. pombe wild type strain in YPD or YES medium, respectively, to a density of approx. 3 * 108 cells/ml.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA purified with Blood & Cell Culture DNA Midi Kit (QIAGEN) using 100/G QIAGEN Genomic-tip
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 1000
 
Description HindIII 70% cut
Data processing Library strategy: ORE-seq
bowtie2 (v. 2.4.4) alignment to joint S.cerevisiae/S.pombe genome Parameters "-X 500 --no-discordant --no-mixed --no-unal"
filter multiply mapped reads using samtools view -hf 0x2
Coverage using bamCoverage (deepTools v. 3.5.1)
Genome_build: SacCer3 & EF2
Supplementary_files_format_and_content: BigWig file of genomic coverage
 
Submission date Nov 18, 2021
Last update date Jan 01, 2023
Contact name Tobias Straub
E-mail(s) tstraub@med.uni-muenchen.de
Organization name LMU Munich
Department Biomedical Center, Bioinformatics
Street address Großhadener Str. 9
City Martinsried
ZIP/Postal code 82152
Country Germany
 
Platform ID GPL30979
Series (1)
GSE189142 ORE-seq: genome-wide absolute occupancy measurement by restriction enzyme accessibilities
Relations
BioSample SAMN23284982
SRA SRX13167273

Supplementary file Size Download File type/resource
GSM5695177_BY6_HindIII_EcoRI-norm_70_pct_cut_X_coverage.bw 2.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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