|
| Status |
Public on Mar 12, 2016 |
| Title |
WT_1_MNase |
| Sample type |
SRA |
| |
|
| Source name |
WT_MNase
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: W303 auxotroph
genotype/variation: wild-type
matched wild type sample: (-)
|
| Treatment protocol |
cells were treated with zymolyase and spheroplasts were treated with MNase and ExoIII to produce nucleosome ladders corresponding to roughly 80% mononucleosomes
|
| Growth protocol |
log cells were grown to OD600 0.4 to 0.6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified by phenol/chloroform and mononucleosome size fragments were purified from an agarose gel for library construction
TruSeq protocol (Illumina) was followed
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Tophat2
Mapped reads were filtered using SAMtools flags -f 3 -F 256
Dyads were calculated by taking the midpoint of paired-end reads from fragments between 100 and 200 bp
Data were normalized such that average value at a genomic position was 1.0
Between-strain comparisons were done using best-matched MNase digests. For isw2-related parent strains, wild-type 2 is best-matched. For ume6-related strains, wild-type 1 is best-matched. For WT +Chd1Ume6, wild-type 1 is best-matched.
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: coverage file with tab-delimited chromosome/position/normalized dyad counts
|
| |
|
| Submission date |
Sep 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey N McKnight |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oregon
|
| Department |
Institute of Molecular Biology
|
| Lab |
McKnight Lab
|
| Street address |
1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge
|
| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97408 |
| Country |
USA |
| |
|
| Platform ID |
GPL9134 |
| Series (2) |
| GSE72570 |
Sequence-Targeted Nucleosome Sliding in vivo - Nucleosome Mapping |
| GSE72572 |
Sequence-Targeted Nucleosome Sliding in vivo |
|
| Relations |
| BioSample |
SAMN04024958 |
| SRA |
SRX1176419 |
