|
Status |
Public on Jan 01, 2019 |
Title |
419R_low |
Sample type |
SRA |
|
|
Source name |
whole organism
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
tissue: whole organism strain: YSK419 genotype: W303 ISW1-aid*-9myc-HphNT Padh1-Os.TIR1:URA3
|
Treatment protocol |
30 minutes auxin (3-IAA)
|
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 |
SAMN09375162 |
SRA |
SRX4174692 |