|
| Status |
Public on Mar 19, 2010 |
| Title |
WT_G1_37C_Nucleosomes |
| Sample type |
SRA |
| |
|
| Source name |
WT W303
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
synchronized: G2 / nocodazole
temperature: 37C
fragmentation: micrococcal nuclease
|
| Treatment protocol |
Cells were arrested for two hours at G1 in 0.25 µg/ml alpha factor at permissive temperature (23C) and then shifted for two additional hours at restrictive temperature (37C). Mononucleosomes were prepared from cells that were cross-linked with .1% formaldehyde for 30 minutes and quenched with 125 mM glycine. After cross-linking, the cells were spheroplasted and treated with 80 units of micrococcal nuclease to generate mononucleosome fragments.
|
| Growth protocol |
Yeast were grown at the permissive temperature (23C) in rich medium for all experiments.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mononucleosomes were prepared from 1.5 x 10^9 cells that were cross-linked with .1% formaldehyde for 30 minutes and quenched with 125 mM glycine. After cross-linking, the cells were spheroplasted and treated with 80 units of micrococcal nuclease to generate mononucleosome fragments. 50 ng of isolated mononucleosomal DNA fragments were prepared for sequencing using the genomic DNA sample preparation kit (Illumina) according to the manufacturer's instructions.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
MNase digestion of WT mononucleosomal fragments at heatshock temperature
|
| Data processing |
Mapview alignment files were generated with the program MAQ, which was fed the raw data in the Illumina fastq format, and a build of the S. cerevisiae S288C from SGD (Jan 2006). All of the default options were used, except that the maximum number of allowed mismatches was raised to 3. All further processed data was generated using in-house analysis methods described in the GSE16926_nucleosomes_2009_supp.pdf.
|
| |
|
| Submission date |
Aug 19, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew Lucas Eaton |
| E-mail(s) |
[email protected]
|
| Phone |
(919) 613-8616
|
| URL |
http://macalpine-lab.duhs.duke.edu/
|
| Organization name |
Duke University
|
| Department |
Pharmacology & Cancer Biology
|
| Lab |
MacAlpine Lab
|
| Street address |
LSRC Room C315, Research Dr
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL9134 |
| Series (1) |
| GSE16926 |
ORC precisely positions nucleosomes at origins of replication |
|
| Relations |
| SRA |
SRX016027 |
| BioSample |
SAMN00008214 |
