|
| Status |
Public on Mar 31, 2015 |
| Title |
rsc1 null rsc2ts |
| Sample type |
RNA |
| |
|
| Source name |
rsc1 null rsc2ts
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YBC1111
genotype/variation: rsc1 null rsc2ts
|
| Growth protocol |
Cells were grown in standard synthetic complete media with 2% glucose at 30C until an optical density at 600 nm of 0.8. Harvested cells were frozen in liquid nitrogen and stored at -80C until ready for processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were pulverized in liquid nitrogen. Approximately 30 mg of lysed cell material was used with the Ambion Mirvana RNA isolation kit following the manufacturer's protocol to isolate total RNA.
|
| Label |
none
|
| Label protocol |
None
|
| |
|
| Hybridization protocol |
Total RNA samples were fragmented and combined with Agilent Hi-RPM GE Hybridization kit (cat#5190-0403) reagents. These samples were hybridized to the array slides at 65C for 17 hr. The slides were washed in 6x SSPE, 0.005% N-lauroylsarcosine for one min at room temperature and in 0.06x SSPE, 0.005% N-lauroylsarcosine for 1 min at 31C. The slides were then incubated with 0.025mg/mL primary monoclonal mouse anti-RNA DNA hybrid antibody available in a hybridoma cell line from ATCC (HB-8730). This was diluted in 500uL of SB+BSA (100mM MES, pH 6.6, 1M NaCl, 0.05% Tween 20, and 1 mg/mL BSA). The 60 min incubation was at 25C. After this incubation the slides were washed four times for three min in NSWB (6xSSPE, 0.01% Tween 20). The secondary Cy3-labeled goat anti-mouse antibody (KPL, cat#078-18-061) was used at a concentration of 3ug/mL in 500uL of SB+BSA. The slides were incubated with the secondary antibody for 60 min at 25C. Finally the slides are washed four times for three min in NSWB at room temperature.
|
| Scan protocol |
Arrays were scanned in an Agilent G2505B Microarray Scanner using extended dynamic range software. Feature extraction of the scanned images was performed using Agilent Feature Extraction Software Version 9.5.1.
|
| Description |
6370X2; 6371X2; 6372X2
YBC1111 sample
|
| Data processing |
Raw feature intensities from three replicates were quantile normalized, median scaled to the mean value of the zebra fish non-hybridizing sequence probes which themselves were scaled to 1, and the combined expression values converted to log2 values. Probe sequences were mapped to Saccharoymyces cerevisisiae genome release 64 (UCSC sacCer3) and were then associated with the corresponding processed feature score. Processing was done with the BioToolBox (http://code.google.com/p/biotoolbox) programs process_microarray and map_oligo_data2gff.
Quantile normalized log2 values representing absolute expression relative to the mean signal of non-hybridizing zebra fish sequence probes.
|
| |
|
| Submission date |
Feb 04, 2015 |
| Last update date |
Mar 31, 2015 |
| Contact name |
Timothy J Parnell |
| E-mail(s) |
timothy.parnell@hci.utah.edu
|
| Organization name |
Huntsman Cancer Institute
|
| Street address |
2000 Circle of Hope
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL19733 |
| Series (2) |
| GSE65591 |
RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [HybMap microarray] |
| GSE65594 |
The Chromatin Remodelers RSC and ISW1 Display Functional and Chromatin-based Promoter Antagonism |
|
