|
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 |