|
| Status |
Public on Jan 01, 2019 |
| Title |
Isw1_1m_ChEC |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YSK454
genotype: W303 ISW1-3xFLAG-MNase-HphMX
antibody: N/A
|
| Treatment protocol |
1 minute of 2.5 mM calcium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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 |
| |
|
| 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 and then, the signal for each protein tested was normalized to the signal of free MNase using a Bayesian approach
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 |
Oct 30, 2018 |
| Last update date |
Jan 02, 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 |
SAMN10348728 |
| SRA |
SRX4957401 |
