|
Status |
Public on Mar 01, 2004 |
Title |
021-680680 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
HA-TBP Reference/un-purified DNA (CH1)
|
Organism |
Saccharomyces cerevisiae |
Extracted molecule |
genomic DNA |
|
|
Channel 2 |
Source name |
HA-TBP Purified ChIP DN (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 |