|
| Status |
Public on Jun 01, 2018 |
| Title |
Abf1_Sth1aa_V_lowMNase |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YSK312
genotype/variation: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX ABF1-FRB-KanMX
|
| Treatment protocol |
No rapamycin.
|
| Growth protocol |
Cells were grown at 30 degrees in 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 150 bp and extended by 50 bp.
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: bigWig files were obtained using HTSStation (http://htsstation.epfl.ch).
|
| |
|
| Submission date |
Apr 26, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
SAMN06840563 |
| SRA |
SRX2766277 |
