|
| Status |
Public on Jan 10, 2006 |
| Title |
24a_null |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
strain yjdi363
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain yjdi363 GAL1-TAF1 WT + taf1 ts2
|
| Biomaterial provider |
Pugh Lab, Penn State University
|
| Treatment protocol |
Galactose induction of TAF1 mutants and heat shock (37C), see below.
|
| Growth protocol |
Cells were grown in CSM-LEU + 3% raffinose to OD600 of ~0.7. Galactose was added to 2% and cultures were incubated for 30 minutes at 25ûC. Cultures were then rapidly shifted to 37ûC by adding warm media and placing in a 37ûC shaker incubator for 45 minutes before harvest at 4ûC.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Holstege et al. 1998. Cell. 95:717-28
|
| Label |
Cy5
|
| Label protocol |
Chitikila et al. 2002. Mol Cell. 10:871-82
|
| |
|
| Channel 2 |
| Source name |
strain yjdi381
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain yjdi381 GAL1-taf1::KanMX6 + taf1 ts2
|
| Biomaterial provider |
Pugh Lab, Penn State University
|
| Treatment protocol |
see above
|
| Growth protocol |
see above
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
see above
|
| Label |
Cy3
|
| Label protocol |
[Chitikila et al. 2002. Mol Cell. 10:871-82
|
| |
|
| |
| Hybridization protocol |
see above
|
| Scan protocol |
Chitikila et al. 2002. Mol Cell. 10:871-82
|
| Description |
no additional information needed
|
| Data processing |
MeanFRG- MedianBCK>S.D. BCK, <26% saturation. Ratio of Test/Ref.
|
| |
|
| Submission date |
Jul 25, 2005 |
| Last update date |
Jan 10, 2006 |
| Contact name |
Jordan D Irvin |
| E-mail(s) |
jdi106@psu.edu
|
| Phone |
814 863-8594
|
| Fax |
814 863-8594
|
| Organization name |
Penn State University
|
| Department |
Biochemistry
|
| Lab |
Frank Pugh
|
| Street address |
452 N Frear
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL1220 |
| Series (1) |
| GSE3006 |
Genome-wide transcriptional dependencies on TAF1 functional domains |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
log2 of PRE_VALUE |
| CH1_MEAN |
|
| CH1_BCK_MEDIAN |
CH1 (F635) background median fluorescence intensity |
| CH1_BCK_SD |
CH1 (F635) background fluorescence intensity standard deviation |
| CH1_%SAT |
%of feature pixels greater than two standard deviations over the background |
| CH2_MEAN |
|
| CH2_BCK_MEDIAN |
CH2 (F532) background median fluorescence intensity |
| CH2_BCK_SD |
CH2 (F532) background fluorescence intensity standard deviation |
| CH2_%SAT |
%of feature pixels greater than two standard deviations over the background |
| Flags |
Features which were flagged in the GenePix Pro 4.0 analysis software have a value < 0 |
| PRE_VALUE |
Unnormalized Ratio of (CH1_Median - CH1_BCK_Median)/(CH2_Median - CH2_BCK_Median); see methods and publication for full treatment and duplicate normalized values; all ratios used in analysis should reflect Heat Shocked / Mock Treated |
