|
| Status |
Public on Jan 01, 2023 |
| Title |
BY6_AluI_90_pct_cut_X |
| Sample type |
SRA |
| |
|
| Source name |
S. cerevisiae/S. pombe cells
|
| Organisms |
Schizosaccharomyces pombe; Saccharomyces cerevisiae |
| Characteristics |
restriction enzyme: AluI
digestion degree[%]: 90
|
| 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 |
Illumina HiSeq 1500 |
| |
|
| Description |
AluI 90% 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 |
GPL30978 |
| Series (1) |
| GSE189142 |
ORE-seq: genome-wide absolute occupancy measurement by restriction enzyme accessibilities |
|
| Relations |
| BioSample |
SAMN23284994 |
| SRA |
SRX13167261 |
