|
| Status |
Public on Jun 01, 2014 |
| Title |
mec1_100_35min_rep2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
BrdU IP DNA from S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: mec1-100
drug: no drug
time point: 35 minutes
antibody: BrdU antibody (Invitrogen, catalog#033900, lot#1462116A)
|
| Treatment protocol |
cells were arrested for 4 hours at 23 degrees C with 7.5 nM alpha factor and then released into fresh media containing 200ug/ml Pronase, 400 ug/ml BrdU
|
| Growth protocol |
Cells were grown in YEPD to OD ~0.5
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 25ml of culture using standard phenol chloroform extraction
|
| Label |
Cy5
|
| Label protocol |
Standard Nimblegen Protocol
|
| |
|
| Channel 2 |
| Source name |
Total DNA from WT G1-arrested S. cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: WT
time point: G1 arrest
|
| Treatment protocol |
cells were arrested for 4 hours at 23 degrees C with 7.5 nM alpha factor
|
| Growth protocol |
Cells were grown in YEPD to OD ~0.5
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from 25ml of culture using standard phenol chloroform extraction
|
| Label |
Cy3
|
| Label protocol |
Standard Nimblegen Protocol
|
| |
|
| |
| Hybridization protocol |
Standard Nimblegen Protocol
|
| Scan protocol |
Genepix Personal 4100A Scanner (Axon Instruments)
|
| Description |
SAMPLE 18
|
| Data processing |
HU array experiments (arrays 1-6) were within array normalized as in Knott et al. BMC Bioinformatics 2009. Within array normalization for time course experiments (arrays 7-18) was performed as previously described in Knott et al Cell 2012. Final data for all samples is normalized as indicated above and median smoothed over a 2500bp window.
|
| |
|
| Submission date |
Feb 18, 2014 |
| Last update date |
Jun 01, 2014 |
| Contact name |
Jared M Peace |
| Organization name |
University of Southern California
|
| Department |
Molecular and Computational Biology
|
| Lab |
Oscar Aparicio
|
| Street address |
1050 Childs Way RRI 203
|
| City |
Los Angeles |
| State/province |
CA - California |
| ZIP/Postal code |
90089 |
| Country |
USA |
| |
|
| Platform ID |
GPL14887 |
| Series (2) |
| GSE55130 |
Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome [array] |
| GSE55156 |
Rif1 regulates initiation timing of late replication origins throughout the S. cerevisiae genome |
|
