|
| Status |
Public on Mar 01, 2004 |
| Title |
024-680680 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Untagged Strain Reference/un-purified DNA (CH1)
|
| Organism |
Saccharomyces cerevisiae |
| Extracted molecule |
genomic DNA |
| |
|
| Channel 2 |
| Source name |
Untagged Strain Purified ChIP DNA (CH2)
|
| Organism |
Saccharomyces cerevisiae |
| Extracted molecule |
genomic DNA |
| |
|
| |
| Description |
Strains were grown in CSM media at 25ûC to OD600 = ~0.8. Then the cultures were shifted to 37ûC with an equal volume of heated media. After 5 min. at 37ûC, cells were cooled back to 25ûC and cross-linked with 1% formaldehyde for 15 minutes. Cross-linkage was quenched with 0.25M Glycine for 5 minutes. Cells were harvested at 4ûC. See methods and publication for details on chromatin immunprecipitation, non-specific amplification and intergenic array hybridization.
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.
Keywords = Saccharomyces cerevisiae
|
| |
|
| Submission date |
Nov 25, 2003 |
| Last update date |
Feb 20, 2008 |
| Contact name |
Frank Pugh |
| E-mail(s) |
bfp2@psu.edu
|
| Organization name |
The Pennsylvania State University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Pugh Laboratory
|
| Street address |
452 North Frear Laboratory
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL760 |
| Series (2) |
| GSE886 |
Identification and distinct regulation of yeast TATA-box containing genes |
| GSE2488 |
Full and partial genome-wide assembly and disassembly of the yeast transcription machinery in response to heat shock |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
log ratio (log2 of PRE_VALUE) |
| CH1_MEDIAN |
CH1 (F635) median fluorescence intensity |
| 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_MEDIAN |
CH2 (F532) median fluorescence intensity |
| 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 (CH2_Median - CH2_BCK_Median)/(CH1_Median - CH1_BCK_Median) where CH2 is the enriched sample and CH1 is the Reference sample; see methods and publication for full treatment and duplicate normalized values |
