|
| Status |
Public on Feb 19, 2012 |
| Title |
mcs6-as2_cdk9-as_CAK1_rep3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
total RNA from an mcs6 and cdk9 analog-sensitive double-mutant in a CAK1::ura4 background grown in the presence of 30 μM 3-MB-PP1 ATP analog
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
treatment: 30 μM 3-MB-PP1 in DMSO
genotype: mcs6 and cdk9 analog-sensitive double-mutant in a CAK1::ura4 background
|
| Treatment protocol |
30 μM 3-MB-PP1 ATP analog was added to the specified treatment conditions
|
| Growth protocol |
A culture of 100ml was grown at 32°C in YES medium until mid-log phase, pelleted and snap-frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared by acidic phenol extraction at 65°C for 1 hour with brief vortexing every 10 minutes. The water phase was re-extracted with acidic phenol-chloroform-IAA (24:24:1) and the RNA precipitated. About 250 µg of RNA were purified on Qiagen RNeasy column and eluted with 30 µl H20.
|
| Label |
Cy3
|
| Label protocol |
For each sample, 500 µg of total RNA was converted into labeled cRNA with nucleotides coupled to a fluorescent dye using the Low RNA Input Linear Amplification Kit (Agilent Technologies).
|
| |
|
| Channel 2 |
| Source name |
total RNA from an mcs6 and cdk9 analog-sensitive double-mutant in a CAK1::ura4 background grown without ATP analog
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: mcs6 and cdk9 analog-sensitive double-mutant in a CAK1::ura4 background
treatment: DMSO only (control)
|
| Treatment protocol |
30 μM 3-MB-PP1 ATP analog was added to the specified treatment conditions
|
| Growth protocol |
A culture of 100ml was grown at 32°C in YES medium until mid-log phase, pelleted and snap-frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared by acidic phenol extraction at 65°C for 1 hour with brief vortexing every 10 minutes. The water phase was re-extracted with acidic phenol-chloroform-IAA (24:24:1) and the RNA precipitated. About 250 µg of RNA were purified on Qiagen RNeasy column and eluted with 30 µl H20.
|
| Label |
Cy5
|
| Label protocol |
For each sample, 500 µg of total RNA was converted into labeled cRNA with nucleotides coupled to a fluorescent dye using the Low RNA Input Linear Amplification Kit (Agilent Technologies).
|
| |
|
| |
| Hybridization protocol |
750 ng of labeled cRNA was hybridized per sample, according to standard Agilent protocols.
|
| Scan protocol |
Microarrays were scanned using an Agilent Microarray Scanner G2565CA (Agilent Technologies)
|
| Description |
biological replicate 1 of 2
|
| Data processing |
Spot quantification was carried out using Feature Extraction software v9.5 (Agilent Technologies). Following quantification, the microarray data was lowess-normalized and an expression ratio was calculated for each microarray feature by dividing the signal intensity of the treatment channel (analog inhibitor) by the control channel (no inhibitor).
|
| |
|
| Submission date |
Feb 19, 2011 |
| Last update date |
Feb 19, 2012 |
| Contact name |
Harm van Bakel |
| E-mail(s) |
harm.vanbakel@mssm.edu
|
| Organization name |
Mount Sinai School of Medicine
|
| Department |
Genetics and Genomic Sciences
|
| Lab |
Bakel Lab
|
| Street address |
One Gustave L. Levy Place, Box 1498
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL8679 |
| Series (1) |
| GSE27425 |
Fission yeast Cdk7 controls gene expression through both its CAK and CTD kinase activities |
|
