|
| Status |
Public on Dec 15, 2016 |
| Title |
H4_Input_MNase_100U_Replicate_1 |
| Sample type |
SRA |
| |
|
| Source name |
S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain name: YDC439
genotype: MATa ade2-1 leu2-3,112 trp1-1 ura3-1 hht1-hhf1delta::LEU2 URA3::HHT2-HA-HHF2
|
| Treatment protocol |
Cells were cross-linked with 1% formaldehyde for 15 min at room temperature and then treated with 0.5M glycine for 5 min. Stored as pellets at -80C.
|
| Growth protocol |
Cells were grown to mid-log phase in Synthetic Complete (SC) medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were prepared from cross-linked cells and digested with different amounts of MNase (units given in filenames). For IP we used a monoclonal anti-HA antibody (see Methods 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 |
| |
|
| Description |
Biological replicate 1
|
| 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 50 and 200bp.
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 |
Jun 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Razvan V. Chereji |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE83123 |
MNase-sensitive complexes in yeast: nucleosomes and non-histone barriers |
|
| Relations |
| BioSample |
SAMN05216626 |
| SRA |
SRX1831773 |
