|
| Status |
Public on Jan 16, 2019 |
| Title |
isw1∆ chd1∆ cells, 50U MNase, Experiment 1 |
| Sample type |
SRA |
| |
|
| Source name |
isw1∆ chd1∆ cells, 50U MNase, Experiment 1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain name: YJO484
genotype: MATa ade2-1 can1-100 his3-11,15 leu2-3,112 trp1-1 ura3-1 RAD5+ isw1-delta::ADE2 chd1-delta::HIS5
|
| Growth protocol |
Cells were grown to mid-log phase in Synthetic Complete (SC) medium, harvested by filtration and cell pellets were stored at -80C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were prepared and digested with different amounts of MNase (units given in filenames, see paper for details).
The DNA was repaired using the DNA PreCR kit from New England Biolabs. Paired-end libraries were constructed and indexed using Illumina kits from NEB (E7370 and E7335).
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequences were aligned to the yeast genome (sacCer3) using Bowtie2 with default settings.
Reads were size selected, and we kept all reads with the lengths between 120-180 bp (mono-nucleosomes) and 250-350 bp (di-nucleosomes).
Genome-wide coverage profiles were computed in MATLAB, and they were normalized such that the average coverage for every chromosome is 1.
IGV tracks (tdf files) were generated using igvtools.
Genome_build: sacCer3
Supplementary_files_format_and_content: tdf files containing the normalized occupancy profiles, for the IGV browser
|
| |
|
| Submission date |
Jul 23, 2018 |
| Last update date |
Jan 16, 2019 |
| Contact name |
Razvan V. Chereji |
| E-mail(s) |
razvan.chereji@nih.gov
|
| Phone |
301-435-8670
|
| Organization name |
National Institutes of Health
|
| Department |
NICHD
|
| Lab |
David J. Clark Lab
|
| Street address |
6 Center Drive, Room 2A14
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE117514 |
Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination |
|
| Relations |
| BioSample |
SAMN09703674 |
| SRA |
SRX4417513 |
