|
| Status |
Public on Jun 01, 2018 |
| Title |
Rap1aa_R_Rsc8_ChEC |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YSK512
genotype/variation: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 RAP1-FRB-RAP1-LEU2 PREB1-3xFLAG-MNase-URA3
|
| Treatment protocol |
60 minutes rapamycin
|
| Growth protocol |
cells were grown at 30 degrees in YPD to OD600=0.7
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was prepared as described in Zentner et al., 2015 (PMID: 26490019)
libraries were prepared as described in Zentner et al., 2015 (PMID: 26490019)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Chromatin Endogenous Cleavage (ChEC)
|
| Data processing |
Library strategy: ChEC-seq
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 150 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 |
May 09, 2018 |
| Last update date |
Jun 01, 2018 |
| Contact name |
Slawomir Kubik |
| E-mail(s) |
[email protected]
|
| 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 (2) |
| GSE98259 |
Promoter DNA sequence guides factors that position the +1 nucleosome and facilitate TBP binding [sequencing] |
| GSE98260 |
Promoter DNA sequence guides factors that position the +1 nucleosome and facilitate TBP binding |
|
| Relations |
| BioSample |
SAMN09100610 |
| SRA |
SRX4061757 |
