|
Status |
Public on Feb 19, 2012 |
Title |
mcs6-as2_rep3 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
total RNA from an mcs6-as analog-sensitive mutant 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-as analog-sensitive mutant
|
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-as analog-sensitive mutant grown without ATP analog
|
Organism |
Schizosaccharomyces pombe |
Characteristics |
genotype: mcs6-as analog-sensitive mutant 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 |
|