|
| Status |
Public on Jan 01, 2019 |
| Title |
387R_low |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tissue: whole organism
strain: HHY190
genotype: W303 SNF2-FRB-KanMX tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1
|
| Treatment protocol |
60 minutes rapamycin
|
| Growth protocol |
cells were grown at 30 degrees i YPD to mid-log phase before treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin for MNase digestion was prepared essentially as described in Kubik et al., 2015 (GSE73337) (PMID: 26545077)
Libraries were prepared essentially as described in Henikoff et al., 2011 (GSE30551) (PMID: 22025700)
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For nucleosome occupancy tracks each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
For ChEC-seq experiments the mapped reads were extended by 1 bp only to indicate cut sites
For ChIP-seq the reads were shifted by 100 bp and extended by 50 bp
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)
|
| |
|
| Submission date |
Jun 06, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Slawomir Kubik |
| E-mail(s) |
Slawomir.Kubik@unige.ch
|
| Organization name |
University of Geneva
|
| Department |
Molecular Biology Department
|
| Street address |
quai Ernest-Ansermet 30
|
| City |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE115412 |
Opposing chromatin remodeler activities control initiation frequency and start site selection |
|
| Relations |
| BioSample |
SAMN09375151 |
| SRA |
SRX4174680 |
