|
| Status |
Public on Mar 19, 2010 |
| Title |
WT_G2_ORC_rep1-2 |
| Sample type |
SRA |
| |
|
| Source name |
WT W303
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
synchronized: G2 / nocodazole
temperature: 23C
antibody: polyclonal ORC
fragmentation: sonication
|
| Treatment protocol |
Cells were arrested at G2/M in 10 µg/ml nocodazole for two hours.
|
| Growth protocol |
wild-type (W303) and mutant (orc1-161) yeast strains were grown at the permissive temperature (23C) in rich medium for all experiments.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP extracts were prepared from 5x10^8 cells. An anti-ORC polyclonal antibody was used for the ChIP. 500 ng of the immunoprecipitated DNA was prepared for sequencing using the genomic DNA sample preparation kit (Illumina) according to the manufacturer's instructions and was size-selected (250-350 bp) after the addition of the adapter oligomers and the PCR amplication step.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
ChIP against ORC
GSM424494_acs_locations.bed: a file with our calls for exact ORC positions based on both sequence motifs and the ChIP-seq data (ORC binds a motif called the ACS)
|
| 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 |
Jul 02, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew Lucas Eaton |
| E-mail(s) |
matthew.eaton@duke.edu
|
| 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 |
SRX016026 |
| BioSample |
SAMN00008213 |
