|
| Status |
Public on Jun 08, 2012 |
| Title |
chd1D_H3K36me3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
chd1D_H3K36me3_IP
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: GHY2317
genotype/variation: chd1D
antibody: H3K36me3
antibody/vendor: Abcam
|
| Treatment protocol |
Cells were fixed in 1% formaldehyde.
|
| Growth protocol |
WT and mutant cells were grown to log phase in YPD media at 30°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed in water, digested with zymolyase and then treated with micrococcal nuclease. Immunoprecipitations were performed with extract equivalent to 100 ml of cell culture in the following volumes: 10μl anti-H3K36me3 (Abcam polyclonal), or 7μl anti-H3K4me3 (Millipore monoclonal). Immunoprecipitation, washing, protein degradation, and DNA isolation were performed as previously described [2].
|
| Label |
Cy3
|
| Label protocol |
DNA samples were amplified, with a starting amount of up to 75 ng for ChIP samples, using the DNA linear amplification method described previously [1]. 2.5 micrograms of aRNA produced from the linear amplification were labeled via the amino-allyl method as described on www.microarrays.org.
|
| |
|
| Channel 2 |
| Source name |
chd1D_H3K36me3_input
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: GHY2317
genotype/variation: chd1D
antibody: none
|
| Treatment protocol |
Cells were fixed in 1% formaldehyde.
|
| Growth protocol |
WT and mutant cells were grown to log phase in YPD media at 30°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed in water, digested with zymolyase and then treated with micrococcal nuclease. Immunoprecipitations were performed with extract equivalent to 100 ml of cell culture in the following volumes: 10μl anti-H3K36me3 (Abcam polyclonal), or 7μl anti-H3K4me3 (Millipore monoclonal). Immunoprecipitation, washing, protein degradation, and DNA isolation were performed as previously described [2].
|
| Label |
Cy5
|
| Label protocol |
DNA samples were amplified, with a starting amount of up to 75 ng for ChIP samples, using the DNA linear amplification method described previously [1]. 2.5 micrograms of aRNA produced from the linear amplification were labeled via the amino-allyl method as described on www.microarrays.org.
|
| |
|
| |
| Hybridization protocol |
Labeled probes (a mixture of Cy5 labeled input and Cy3 labeled ChIPed material) were hybridized onto an Agilent yeast 4x44 whole genome array. The arrays were scanned at 5 micron resolution with the Agilent array scanner. Image analysis and data normalization were performed as previously described [1].
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent High Resolution C fluorescent scanner at 5 micron resolution and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.
|
| Data processing |
After background correction and removal of flagged values, data was block normalized by dilation and log base 2 ratios (Cy3/Cy5) were calculated to produce the values given in the data table.
|
| |
|
| Submission date |
Jun 05, 2012 |
| Last update date |
Jun 08, 2012 |
| Contact name |
Grant A Hartzog |
| E-mail(s) |
[email protected]
|
| Phone |
8314595826
|
| Fax |
8314593139
|
| Organization name |
UC Santa Cruz
|
| Department |
MCD Biology
|
| Street address |
349 Sinsheimer Labs
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL4131 |
| Series (2) |
| GSE38492 |
A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast (H3K4me3 or H3K36me3 to input) |
| GSE38540 |
A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast |
|
